Rematch documents by content fingerprint on upload and session open.

Re-uploading the same PDF attaches bytes to the existing document (keeping
evidence) instead of creating a twin. On restore, merge duplicate fingerprint
groups and migrate annotations onto the evidence-bearing primary.

src/app/App.tsx

@@ -38,6 +38,7 @@ import { CaptureLinkPersister } from "./forms/CaptureLinkPersister";
 import { loadCaptureState } from "./forms/capture-persistence";
 import { FormsApp } from "./forms/FormsApp";
 import { ReviewLayout } from "./ReviewLayout";
+import { DocumentFingerprintReconciler } from "./sessions/DocumentFingerprintReconciler";
 
 import {
   CreateFirstSession,
@@ -176,6 +177,7 @@ function SessionScopedTree({ mode }: { mode: AppMode }) {
         ? { initialLinks: restoredCapture.evidenceLinks }
         : {})}
     >
+      <DocumentFingerprintReconciler />
       <CaptureLinkPersister sessionId={sessionId} />
       {mode === "forms" ? (
         <FormsApp

src/app/sessions/DocumentFingerprintReconciler.tsx

@@ -0,0 +1,50 @@
+/**
+ * On session mount / engine restore, collapse documents that share a content
+ * fingerprint (e.g. evidence-bearing record + re-upload twin after a reload
+ * lost bytes). Retargets the active document when it was a discarded twin.
+ */
+
+import { useEffect, useRef } from "react";
+
+import {
+  useActiveDocumentId,
+  useEngine,
+  useEngineRevision,
+  usePdfByteStore,
+} from "@work/index";
+
+import { mergeDuplicateDocumentsByFingerprint } from "./document-rematch";
+
+export function DocumentFingerprintReconciler() {
+  const engine = useEngine();
+  const byteStore = usePdfByteStore();
+  const revision = useEngineRevision();
+  const { id: activeId, setId } = useActiveDocumentId();
+  const ranForRevision = useRef<number | null>(null);
+
+  useEffect(() => {
+    // Run once after each engine restore/hydrate revision bump.
+    if (ranForRevision.current === revision) return;
+    ranForRevision.current = revision;
+
+    const { remappedIds, documentsRemoved } =
+      mergeDuplicateDocumentsByFingerprint(engine, byteStore);
+
+    if (activeId && remappedIds.has(activeId)) {
+      setId(remappedIds.get(activeId)!);
+      return;
+    }
+
+    // Bytes may have moved onto the still-active primary; force the viewer
+    // to re-resolve the blob URL (same id alone may not remount).
+    if (documentsRemoved > 0 && activeId && byteStore.has(activeId)) {
+      const keep = activeId;
+      setId(null);
+      queueMicrotask(() => setId(keep));
+    }
+    // Intentionally omit activeId from deps: we only reconcile on revision.
+    // eslint-disable-next-line react-hooks/exhaustive-deps -- see above
+  }, [engine, byteStore, revision, setId]);
+
+  return null;
+}

src/app/sessions/SampleSessions.tsx

@@ -21,6 +21,8 @@ import {
   usePdfByteStore,
 } from "@work/index";
 
+import { registerOrRematchDocument } from "./document-rematch";
+
 import manifest from "../../../fixtures/pdfs/manifest.json";
 
 interface Fixture {
@@ -60,16 +62,15 @@ export function SampleSessions() {
         const { document, representation } = await ingestPdf(bytes, {
           filename: fixture.filename,
         });
-        // Push the bytes into the byte store so the viewer can mount them via
-        // the same blob URL machinery used by the upload path. The document
-        // record carries the blob URL on `uri` for the viewer adapter.
+        // Same blob URL machinery as the upload path, with fingerprint rematch
+        // so reloading a sample reattaches to an existing session document.
         const record = byteStore.put(document.id, bytes);
-        engine.documents.register({
+        const outcome = registerOrRematchDocument(engine, byteStore, {
           document: { ...document, uri: record.blobUrl },
           representation,
         });
-        setByFixture((prev) => ({ ...prev, [fixture.id]: document.id }));
-        setId(document.id);
+        setByFixture((prev) => ({ ...prev, [fixture.id]: outcome.documentId }));
+        setId(outcome.documentId);
       } catch (err) {
         setError(err instanceof Error ? err.message : String(err));
       } finally {

src/app/sessions/UploadDropzone.tsx

@@ -6,9 +6,9 @@
  *   1. read each File as bytes,
  *   2. run the source-layer `ingestPdfFromFile` (mints the blob URL
  *      via the session's `PdfByteStore`),
- *   3. register the resulting `{document, representation}` with the
- *      engine,
- *   4. activate the most-recently-uploaded document.
+ *   3. register — or rematch by content fingerprint to an existing
+ *      document (so re-upload reattaches PDF bytes to prior evidence),
+ *   4. activate the most-recently-uploaded / rematched document.
  *
  * Failures (non-PDFs, ingest errors) are surfaced inline above the
  * dropzone; the caller doesn't need a separate toast for them.
@@ -23,10 +23,14 @@ import {
   usePdfByteStore,
 } from "@work/index";
 
+import { registerOrRematchDocument } from "./document-rematch";
+
 interface UploadEntry {
   readonly file: File;
   status: "queued" | "uploading" | "done" | "error";
   error?: string;
+  /** True when upload reattached bytes to an existing fingerprint match. */
+  rematched?: boolean;
 }
 
 export interface UploadDropzoneProps {
@@ -67,10 +71,18 @@ export function UploadDropzone({ onUploaded }: UploadDropzoneProps) {
             entry.file,
             byteStore,
           );
-          engine.documents.register({ document, representation });
+          const outcome = registerOrRematchDocument(engine, byteStore, {
+            document,
+            representation,
+          });
           entry.status = "done";
-          lastDocumentId = document.id;
-          onUploaded?.(document.id);
+          if (outcome.kind === "rematched") {
+            entry.error = undefined;
+            // Surface rematch in the progress list without treating it as failure.
+            (entry as UploadEntry & { rematched?: boolean }).rematched = true;
+          }
+          lastDocumentId = outcome.documentId;
+          onUploaded?.(outcome.documentId);
         } catch (err) {
           entry.status = "error";
           entry.error = err instanceof Error ? err.message : String(err);
@@ -178,7 +190,10 @@ export function UploadDropzone({ onUploaded }: UploadDropzoneProps) {
                       : "#333",
               }}
             >
-              {entry.file.name} — {entry.status}
+              {entry.file.name} —{" "}
+              {entry.status === "done" && entry.rematched
+                ? "done (matched existing document by content hash)"
+                : entry.status}
               {entry.error ? `: ${entry.error}` : ""}
             </li>
           ))}

src/app/sessions/document-rematch.test.ts

@@ -0,0 +1,150 @@
+import { describe, expect, it, vi } from "vitest";
+
+import type { Document, DocumentRepresentation } from "@shared/document";
+import type { DocumentId, RepresentationId } from "@shared/ids";
+import { createEngine } from "@engine/index";
+import { createPdfByteStore } from "@source/index";
+
+import {
+  mergeDuplicateDocumentsByFingerprint,
+  pickPrimaryDocument,
+  registerOrRematchDocument,
+  rekeyByteStore,
+} from "./document-rematch";
+
+function makeDoc(
+  id: string,
+  fingerprint: string,
+  title = "doc.pdf",
+): Document {
+  const now = "2026-07-30T00:00:00.000Z";
+  return {
+    id: id as DocumentId,
+    mediaType: "application/pdf",
+    title,
+    fingerprint,
+    createdAt: now,
+    updatedAt: now,
+  };
+}
+
+function makeRep(docId: string, repId: string): DocumentRepresentation {
+  return {
+    id: repId as RepresentationId,
+    documentId: docId as DocumentId,
+    representationType: "pdf-text",
+    contentHash: "hash",
+    canonicalText: "hello",
+    pageMap: [{ page: 1, width: 1, height: 1 }],
+    offsetMap: [{ page: 1, globalStart: 0, globalEnd: 5, pageLength: 5 }],
+    generatedAt: "2026-07-30T00:00:00.000Z",
+  };
+}
+
+describe("document-rematch", () => {
+  it("rekeys byte store from new id onto existing id", () => {
+    const store = createPdfByteStore({
+      createObjectURL: () => "blob:x",
+      revokeObjectURL: () => {},
+    });
+    const from = "doc_new" as DocumentId;
+    const to = "doc_old" as DocumentId;
+    store.put(from, new Uint8Array([1, 2, 3]));
+    expect(rekeyByteStore(store, from, to)).toBe(true);
+    expect(store.has(from)).toBe(false);
+    expect(store.get(to)?.bytes).toEqual(new Uint8Array([1, 2, 3]));
+  });
+
+  it("registerOrRematch attaches bytes to existing fingerprint and skips twin", () => {
+    const engine = createEngine();
+    const store = createPdfByteStore({
+      createObjectURL: vi.fn(() => `blob:${Math.random()}`),
+      revokeObjectURL: () => {},
+    });
+    const existing = makeDoc("doc_old", "fp-aaa", "old.pdf");
+    engine.documents.register({
+      document: existing,
+      representation: makeRep("doc_old", "rep_old"),
+    });
+
+    const fresh = makeDoc("doc_new", "fp-aaa", "reupload.pdf");
+    store.put("doc_new" as DocumentId, new Uint8Array([9, 9]));
+    const result = registerOrRematchDocument(engine, store, {
+      document: { ...fresh, uri: "blob:new" },
+      representation: makeRep("doc_new", "rep_new"),
+    });
+
+    expect(result.kind).toBe("rematched");
+    if (result.kind !== "rematched") return;
+    expect(result.documentId).toBe("doc_old");
+    expect(engine.documents.list()).toHaveLength(1);
+    expect(store.has("doc_new" as DocumentId)).toBe(false);
+    expect(store.get("doc_old" as DocumentId)?.bytes).toEqual(
+      new Uint8Array([9, 9]),
+    );
+  });
+
+  it("registerOrRematch registers when fingerprint is new", () => {
+    const engine = createEngine();
+    const store = createPdfByteStore({
+      createObjectURL: () => "blob:y",
+      revokeObjectURL: () => {},
+    });
+    const doc = makeDoc("doc_1", "fp-new");
+    store.put("doc_1" as DocumentId, new Uint8Array([1]));
+    const result = registerOrRematchDocument(engine, store, {
+      document: doc,
+      representation: makeRep("doc_1", "rep_1"),
+    });
+    expect(result.kind).toBe("registered");
+    expect(engine.documents.list()).toHaveLength(1);
+  });
+
+  it("mergeDuplicateDocumentsByFingerprint prefers evidence-bearing primary", () => {
+    const engine = createEngine();
+    const store = createPdfByteStore({
+      createObjectURL: vi.fn(() => `blob:${Math.random()}`),
+      revokeObjectURL: () => {},
+    });
+
+    const withEvidence = makeDoc("doc_a", "fp-same", "a.pdf");
+    const withBytesOnly = makeDoc("doc_b", "fp-same", "b.pdf");
+    engine.documents.register({
+      document: withEvidence,
+      representation: makeRep("doc_a", "rep_a"),
+    });
+    engine.documents.register({
+      document: withBytesOnly,
+      representation: makeRep("doc_b", "rep_b"),
+    });
+    store.put("doc_b" as DocumentId, new Uint8Array([7, 7, 7]));
+
+    const ann = engine.annotations.create({
+      documentId: "doc_a" as DocumentId,
+      selectors: [{ type: "TextQuoteSelector", exact: "hello" }],
+      quote: "hello",
+    });
+    engine.evidence.create({
+      annotationIds: [ann.id],
+      commentary: "note",
+    });
+
+    const primary = pickPrimaryDocument(engine, store, [
+      withBytesOnly,
+      withEvidence,
+    ]);
+    expect(primary.id).toBe("doc_a");
+
+    const stats = mergeDuplicateDocumentsByFingerprint(engine, store);
+    expect(stats.groupsMerged).toBe(1);
+    expect(stats.documentsRemoved).toBe(1);
+    expect(engine.documents.list().map((d) => d.id)).toEqual(["doc_a"]);
+    expect(store.get("doc_a" as DocumentId)?.bytes).toEqual(
+      new Uint8Array([7, 7, 7]),
+    );
+    expect(engine.annotations.listByDocument("doc_a" as DocumentId)).toHaveLength(
+      1,
+    );
+    expect(engine.evidence.listByDocument("doc_a" as DocumentId)).toHaveLength(1);
+  });
+});

src/app/sessions/document-rematch.ts

@@ -0,0 +1,213 @@
+/**
+ * Document identity by content fingerprint (SHA-256 of source bytes).
+ *
+ * PDFs and evidence are stored under different lifecycle concerns (bytes in
+ * the byte store / IndexedDB; annotations + evidence in the engine snapshot).
+ * They re-join via `Document.fingerprint` so a re-upload of the same file
+ * attaches bytes to the existing document instead of creating a twin.
+ *
+ * Also collapses accidental duplicates (e.g. upload after a reload lost
+ * bytes but kept the evidence-bearing document record).
+ */
+
+import type { Document, DocumentRepresentation } from "@shared/document";
+import type { DocumentId } from "@shared/ids";
+import type { Engine } from "@engine/index";
+import type { PdfByteStore } from "@source/index";
+
+export type RegisterOrRematchResult =
+  | {
+      readonly kind: "registered";
+      readonly documentId: DocumentId;
+      readonly fingerprint: string | undefined;
+    }
+  | {
+      readonly kind: "rematched";
+      readonly documentId: DocumentId;
+      readonly fingerprint: string;
+      readonly discardedDocumentId: DocumentId;
+    };
+
+function evidenceCount(engine: Engine, documentId: DocumentId): number {
+  return engine.evidence.listByDocument(documentId).length;
+}
+
+function annotationCount(engine: Engine, documentId: DocumentId): number {
+  return engine.annotations.listByDocument(documentId).length;
+}
+
+/**
+ * Prefer the document that already carries user work (evidence / annotations),
+ * then one that already has bytes, then the first seen.
+ */
+export function pickPrimaryDocument(
+  engine: Engine,
+  byteStore: PdfByteStore,
+  candidates: readonly Document[],
+): Document {
+  if (candidates.length === 0) {
+    throw new Error("pickPrimaryDocument: empty candidates");
+  }
+  if (candidates.length === 1) return candidates[0]!;
+
+  const scored = candidates.map((doc) => ({
+    doc,
+    evidence: evidenceCount(engine, doc.id),
+    annotations: annotationCount(engine, doc.id),
+    hasBytes: byteStore.has(doc.id) ? 1 : 0,
+  }));
+  scored.sort((a, b) => {
+    if (b.evidence !== a.evidence) return b.evidence - a.evidence;
+    if (b.annotations !== a.annotations) return b.annotations - a.annotations;
+    if (b.hasBytes !== a.hasBytes) return b.hasBytes - a.hasBytes;
+    return a.doc.createdAt.localeCompare(b.doc.createdAt);
+  });
+  return scored[0]!.doc;
+}
+
+export function findDocumentsByFingerprint(
+  engine: Engine,
+  fingerprint: string,
+): readonly Document[] {
+  if (!fingerprint) return [];
+  return engine.documents.list().filter((d) => d.fingerprint === fingerprint);
+}
+
+/**
+ * Move in-memory / durable bytes from `fromId` onto `toId` and drop `fromId`.
+ */
+export function rekeyByteStore(
+  byteStore: PdfByteStore,
+  fromId: DocumentId,
+  toId: DocumentId,
+): boolean {
+  if (fromId === toId) return byteStore.has(toId);
+  const record = byteStore.get(fromId);
+  if (!record) return byteStore.has(toId);
+  byteStore.put(toId, record.bytes);
+  byteStore.delete(fromId);
+  return true;
+}
+
+/**
+ * After ingest, either register a new document or attach bytes to an existing
+ * one with the same fingerprint (evidence stays on the existing id).
+ */
+export function registerOrRematchDocument(
+  engine: Engine,
+  byteStore: PdfByteStore,
+  input: {
+    readonly document: Document;
+    readonly representation: DocumentRepresentation;
+  },
+): RegisterOrRematchResult {
+  const fingerprint = input.document.fingerprint;
+  if (fingerprint) {
+    const matches = findDocumentsByFingerprint(engine, fingerprint);
+    if (matches.length > 0) {
+      const primary = pickPrimaryDocument(engine, byteStore, matches);
+      rekeyByteStore(byteStore, input.document.id, primary.id);
+
+      // Refresh title/uri on the primary when useful (viewer prefers byte store).
+      const live = byteStore.get(primary.id);
+      if (live || input.document.title) {
+        engine.repos.documents.update({
+          ...primary,
+          ...(input.document.title !== undefined
+            ? { title: input.document.title }
+            : {}),
+          ...(live ? { uri: live.blobUrl } : {}),
+          updatedAt: new Date().toISOString(),
+        });
+      }
+
+      // Never register the discarded twin.
+      return {
+        kind: "rematched",
+        documentId: primary.id,
+        fingerprint,
+        discardedDocumentId: input.document.id,
+      };
+    }
+  }
+
+  engine.documents.register({
+    document: input.document,
+    representation: input.representation,
+  });
+  return {
+    kind: "registered",
+    documentId: input.document.id,
+    fingerprint,
+  };
+}
+
+/**
+ * Collapse documents that share a fingerprint into one primary record.
+ * Migrates annotations onto the primary and copies PDF bytes when present.
+ */
+export function mergeDuplicateDocumentsByFingerprint(
+  engine: Engine,
+  byteStore: PdfByteStore,
+): {
+  readonly groupsMerged: number;
+  readonly documentsRemoved: number;
+  /** secondary documentId → primary documentId */
+  readonly remappedIds: ReadonlyMap<DocumentId, DocumentId>;
+} {
+  const byFp = new Map<string, Document[]>();
+  for (const doc of engine.documents.list()) {
+    if (!doc.fingerprint) continue;
+    const list = byFp.get(doc.fingerprint) ?? [];
+    list.push(doc);
+    byFp.set(doc.fingerprint, list);
+  }
+
+  let groupsMerged = 0;
+  let documentsRemoved = 0;
+  const remappedIds = new Map<DocumentId, DocumentId>();
+
+  for (const [, group] of byFp) {
+    if (group.length < 2) continue;
+    groupsMerged += 1;
+    const primary = pickPrimaryDocument(engine, byteStore, group);
+    const primaryRep =
+      engine.documents.listRepresentations(primary.id)[0] ?? null;
+
+    for (const secondary of group) {
+      if (secondary.id === primary.id) continue;
+
+      rekeyByteStore(byteStore, secondary.id, primary.id);
+      remappedIds.set(secondary.id, primary.id);
+
+      for (const ann of engine.annotations.listByDocument(secondary.id)) {
+        engine.repos.annotations.update({
+          ...ann,
+          documentId: primary.id,
+          ...(primaryRep
+            ? { representationId: primaryRep.id }
+            : ann.representationId !== undefined
+              ? { representationId: ann.representationId }
+              : {}),
+          updatedAt: new Date().toISOString(),
+        });
+      }
+
+      // Drop secondary record (and its representations). Evidence items stay:
+      // they key off annotation ids, which now point at primary.
+      engine.documents.remove(secondary.id);
+      documentsRemoved += 1;
+    }
+
+    const live = byteStore.get(primary.id);
+    if (live) {
+      engine.repos.documents.update({
+        ...engine.documents.get(primary.id)!,
+        uri: live.blobUrl,
+        updatedAt: new Date().toISOString(),
+      });
+    }
+  }
+
+  return { groupsMerged, documentsRemoved, remappedIds };
+}

src/app/sessions/importSessionZip.ts

@@ -154,10 +154,29 @@ export async function importSessionZip(
   const targetByteStore = services.getOrCreateByteStore(targetSessionId);
 
   // 5. Build the document remap.
+  // Prefer fingerprint targets that already hold annotations/evidence so a
+  // re-import reattaches to the "work" document, not an empty twin.
   const docRemap = new Map<DocumentId, DocumentId>();
   const existingByFingerprint = new Map<string, DocumentId>();
+  const fingerprintCandidates = new Map<string, Document[]>();
   for (const doc of targetEngine.documents.list()) {
-    if (doc.fingerprint) existingByFingerprint.set(doc.fingerprint, doc.id);
+    if (!doc.fingerprint) continue;
+    const list = fingerprintCandidates.get(doc.fingerprint) ?? [];
+    list.push(doc);
+    fingerprintCandidates.set(doc.fingerprint, list);
+  }
+  for (const [fp, candidates] of fingerprintCandidates) {
+    const scored = candidates.map((doc) => ({
+      id: doc.id,
+      evidence: targetEngine.evidence.listByDocument(doc.id).length,
+      annotations: targetEngine.annotations.listByDocument(doc.id).length,
+    }));
+    scored.sort((a, b) => {
+      if (b.evidence !== a.evidence) return b.evidence - a.evidence;
+      if (b.annotations !== a.annotations) return b.annotations - a.annotations;
+      return 0;
+    });
+    existingByFingerprint.set(fp, scored[0]!.id);
   }
 
   let documentsAdded = 0;