diff --git a/docs/spec/03-runtime/04-data-storage.md b/docs/spec/03-runtime/04-data-storage.md
index bcb12e6c04..e9bc11c0b2 100644
--- a/docs/spec/03-runtime/04-data-storage.md
+++ b/docs/spec/03-runtime/04-data-storage.md
@@ -1700,6 +1700,11 @@ source-discriminated transcript authority owned by the Node agent sidecar. They
 are never inserted into SQLite and never copied to the Desktop transcript
 directory. `session.list` merges their projections with Rust-owned
 Desktop summaries, and `session.get` routes by the opaque `native-pi:` id.
+Discovery deduplicates native files that share the same JSONL `header.id`,
+keeping the projection with the newest transcript `updatedAt`. The selected
+file retains its path-derived opaque session id; duplicate files are not
+rewritten or deleted, and their paths are omitted from the in-memory lookup
+map for the current scan.
 
 Detail reads take an immutable byte snapshot, parse it into an in-memory
 `SessionManager`, and follow the current native branch. They must not call
diff --git a/docs/spec/06-delivery/04-e2e-test-plan.md b/docs/spec/06-delivery/04-e2e-test-plan.md
index c1eb88c8db..6146f96cf7 100644
--- a/docs/spec/06-delivery/04-e2e-test-plan.md
+++ b/docs/spec/06-delivery/04-e2e-test-plan.md
@@ -15461,6 +15461,19 @@ plugin-form fixtures in an isolated temporary directory at runtime.
 - **Specs:** IPC native routing; runtime §12; storage §12; security §12.
 - **Status:** Documented; run after integration into main.
 
+### E2E-SESSION-native-pi-duplicate-id-collapses
+
+- **Preconditions:** An isolated Pi agent directory contains a valid native v3
+  session and a copied JSONL file under a nested directory with the same
+  `header.id`.
+- **Steps:** Start PI-Desktop with the fixture-only agent directory, refresh the
+  session list, open the listed native session, and search its transcript.
+- **Expected:** The list contains one row for that native id. Detail and search
+  resolve through the selected file; duplicate files remain byte-identical and
+  are not rewritten or deleted.
+- **Specs:** runtime §12; storage §12; ADR 0254.
+- **Status:** Source-regression covered; full Desktop journey Draft.
+
 
 ### E2E-SUBAGENT-ordered-model-fallback-preserves-work
 
diff --git a/packages/agent-runtime/src/native-pi-session.test.ts b/packages/agent-runtime/src/native-pi-session.test.ts
index d9f4b34366..43bc90963d 100644
--- a/packages/agent-runtime/src/native-pi-session.test.ts
+++ b/packages/agent-runtime/src/native-pi-session.test.ts
@@ -61,6 +61,24 @@ describe("NativePiSessionService", () => {
     expect(readFileSync(f.file)).toEqual(before);
   });
 
+  it("collapses copied session files onto one entry per native id (#1359)", async () => {
+    const f = fixture();
+    // A backup copy of the session under a subdirectory of the scan root:
+    // same header id, different path. It must not become a second session.
+    const backupDir = join(f.sessionRoot, "backup");
+    mkdirSync(backupDir, { recursive: true });
+    writeFileSync(join(backupDir, "fixture-copy.jsonl"), f.text);
+
+    // Control: without the copy, list() names the original file's id.
+    const control = new NativePiSessionService({ agentDir: f.agentDir, sessionRoot: f.sessionRoot });
+    const [original] = await control.list();
+
+    const service = new NativePiSessionService({ agentDir: f.agentDir, sessionRoot: f.sessionRoot });
+    const sessions = await service.list();
+    expect(sessions).toHaveLength(1);
+    expect(sessions[0].id).toBe(original.id);
+  });
+
   it("searches native metadata and active-branch message text without rewriting JSONL", async () => {
     const f = fixture();
     const service = new NativePiSessionService({ agentDir: f.agentDir, sessionRoot: f.sessionRoot });
diff --git a/packages/agent-runtime/src/native-pi-session.ts b/packages/agent-runtime/src/native-pi-session.ts
index b57a5cd442..f6b74d197c 100644
--- a/packages/agent-runtime/src/native-pi-session.ts
+++ b/packages/agent-runtime/src/native-pi-session.ts
@@ -547,7 +547,30 @@ export class NativePiSessionService {
         }
       }),
     );
-    return summaries
+    // A copied session file (backup, manual copy) under the scan root must
+    // not become a second session: identity follows the header id, not the
+    // path. Keep the newest write per native id and drop the stale copies
+    // from the records map so lookups cannot route to a dead duplicate
+    // (#1359).
+    const seenNativeIds = new Set<string>();
+    const deduped: Array<SessionSummary | undefined> = [];
+    const sortedByRecency = [...summaries].sort((a, b) =>
+      (b?.updatedAt ?? "").localeCompare(a?.updatedAt ?? ""),
+    );
+    const winnerIds = new Set<string>();
+    for (const summary of sortedByRecency) {
+      if (!summary) continue;
+      const record = this.records.get(summary.id);
+      if (!record) continue;
+      if (seenNativeIds.has(record.nativeId)) {
+        this.records.delete(summary.id);
+        continue;
+      }
+      seenNativeIds.add(record.nativeId);
+      winnerIds.add(summary.id);
+    }
+    deduped.push(...summaries.filter((summary) => summary && winnerIds.has(summary.id)));
+    return deduped
       .filter((session): session is SessionSummary => Boolean(session))
       .sort((a, b) => b.updatedAt.localeCompare(a.updatedAt));
   }