diff --git a/scripts/e2e/lib/upgrade-survivor/assertions.mjs b/scripts/e2e/lib/upgrade-survivor/assertions.mjs
index b07a36d77afa..23fa623c5902 100644
--- a/scripts/e2e/lib/upgrade-survivor/assertions.mjs
+++ b/scripts/e2e/lib/upgrade-survivor/assertions.mjs
@@ -479,15 +479,9 @@ function assertSessionMetadataMigrated(stateDir) {
   const main = store["agent:main:main"];
   const direct = store["agent:main:+15551234567"];
   const group = store["agent:main:slack:channel:cupgrade"];
-  assert(main?.sessionId === LEGACY_SESSION_MAIN_ID, "main legacy session row missing from SQLite");
-  assert(
-    direct?.sessionId === LEGACY_SESSION_DIRECT_ID,
-    "direct legacy session row missing from SQLite",
-  );
-  assert(
-    group?.sessionId === LEGACY_SESSION_GROUP_ID,
-    "channel legacy session row missing from SQLite",
-  );
+  assert(main?.sessionId === LEGACY_SESSION_MAIN_ID, "main legacy session row missing");
+  assert(direct?.sessionId === LEGACY_SESSION_DIRECT_ID, "direct legacy session row missing");
+  assert(group?.sessionId === LEGACY_SESSION_GROUP_ID, "channel legacy session row missing");
   assert(
     main?.sessionFile === path.join(agentSessionsDir, `${LEGACY_SESSION_MAIN_ID}.jsonl`),
     "main legacy session row still points at the old sessions directory",
@@ -506,7 +500,7 @@ function assertSessionMetadataMigrated(stateDir) {
   );
   assert(
     main.skillsSnapshot?.resolvedSkills === undefined,
-    "heavy resolvedSkills cache was persisted into SQLite session metadata",
+    "heavy resolvedSkills cache was persisted into migrated session metadata",
   );
 }
 
diff --git a/src/commands/doctor-state-migrations.test.ts b/src/commands/doctor-state-migrations.test.ts
index e91c56462323..2f8f80bdf7de 100644
--- a/src/commands/doctor-state-migrations.test.ts
+++ b/src/commands/doctor-state-migrations.test.ts
@@ -629,7 +629,7 @@ describe("doctor legacy state migrations", () => {
     result: Awaited<ReturnType<typeof runLegacyStateMigrations>>;
     targetDir: string;
     legacySessionsDir: string;
-    store: Record<string, { sessionId: string }>;
+    store: Record<string, { sessionId: string; sessionFile?: string }>;
   };
 
   beforeAll(async () => {
@@ -638,8 +638,12 @@ describe("doctor legacy state migrations", () => {
     const legacySessionsDir = writeLegacySessionsFixture({
       root,
       sessions: {
-        "+1555": { sessionId: "a", updatedAt: 10 },
-        "+1666": { sessionId: "b", updatedAt: 20 },
+        "+1555": {
+          sessionId: "a",
+          sessionFile: path.join(root, "sessions", "a.jsonl"),
+          updatedAt: 10,
+        },
+        "+1666": { sessionId: "b", sessionFile: "b.jsonl", updatedAt: 20 },
         "slack:channel:C123": { sessionId: "c", updatedAt: 30 },
         "group:abc": { sessionId: "d", updatedAt: 40 },
         "subagent:xyz": { sessionId: "e", updatedAt: 50 },
@@ -661,7 +665,7 @@ describe("doctor legacy state migrations", () => {
     const targetDir = path.join(root, "agents", "main", "sessions");
     const store = JSON.parse(
       fs.readFileSync(path.join(targetDir, "sessions.json"), "utf-8"),
-    ) as Record<string, { sessionId: string }>;
+    ) as Record<string, { sessionId: string; sessionFile?: string }>;
 
     migratedLegacySessionsCase = { result, targetDir, legacySessionsDir, store };
   });
@@ -676,6 +680,8 @@ describe("doctor legacy state migrations", () => {
     expect(store["agent:main:main"]?.sessionId).toBe("b");
     expect(store["agent:main:+1555"]?.sessionId).toBe("a");
     expect(store["agent:main:+1666"]?.sessionId).toBe("b");
+    expect(store["agent:main:+1555"]?.sessionFile).toBe(path.join(targetDir, "a.jsonl"));
+    expect(store["agent:main:+1666"]?.sessionFile).toBe(path.join(targetDir, "b.jsonl"));
     expect(store["+1555"]).toBeUndefined();
     expect(store["+1666"]).toBeUndefined();
     expect(store["agent:main:slack:channel:c123"]?.sessionId).toBe("c");
diff --git a/src/infra/state-migrations.ts b/src/infra/state-migrations.ts
index 16f20b0cf7ce..34888e69225f 100644
--- a/src/infra/state-migrations.ts
+++ b/src/infra/state-migrations.ts
@@ -2878,6 +2878,7 @@ async function migrateLegacySessions(
     return { changes, warnings };
   }
 
+  const movedSessionFiles = new Map<string, string>();
   const entries = safeReadDir(detected.sessions.legacyDir);
   for (const entry of entries) {
     if (!entry.isFile()) {
@@ -2887,18 +2888,54 @@ async function migrateLegacySessions(
       continue;
     }
     const from = path.join(detected.sessions.legacyDir, entry.name);
-    const to = path.join(detected.sessions.targetDir, entry.name);
+    let to = path.join(detected.sessions.targetDir, entry.name);
     if (fileExists(to)) {
-      continue;
+      const parsed = path.parse(entry.name);
+      to = path.join(detected.sessions.targetDir, `${parsed.name}.legacy-${now()}${parsed.ext}`);
     }
     try {
       fs.renameSync(from, to);
+      movedSessionFiles.set(path.resolve(from), to);
       changes.push(`Moved ${entry.name} → agents/${detected.targetAgentId}/sessions`);
     } catch (err) {
       warnings.push(`Failed moving ${from}: ${String(err)}`);
     }
   }
 
+  if (movedSessionFiles.size > 0) {
+    let rewroteSessionFiles = false;
+    for (const entry of Object.values(merged)) {
+      const rawSessionFile = entry.sessionFile;
+      const legacySessionFile =
+        typeof rawSessionFile === "string"
+          ? path.resolve(detected.sessions.legacyDir, rawSessionFile)
+          : typeof entry.sessionId === "string"
+            ? path.join(detected.sessions.legacyDir, `${entry.sessionId}.jsonl`)
+            : undefined;
+      const movedSessionFile = legacySessionFile
+        ? movedSessionFiles.get(path.resolve(legacySessionFile))
+        : undefined;
+      if (!movedSessionFile) {
+        continue;
+      }
+      entry.sessionFile = movedSessionFile;
+      rewroteSessionFiles = true;
+    }
+    if (rewroteSessionFiles) {
+      const normalized: Record<string, SessionEntry> = {};
+      for (const [key, entry] of Object.entries(merged)) {
+        const normalizedEntry = normalizeSessionEntry(entry);
+        if (normalizedEntry) {
+          normalized[key] = normalizedEntry;
+        }
+      }
+      await saveSessionStore(detected.sessions.targetStorePath, normalized, {
+        skipMaintenance: true,
+      });
+      changes.push("Rewrote migrated session transcript paths");
+    }
+  }
+
   if (legacyParsed.ok && targetReadable) {
     try {
       if (fileExists(detected.sessions.legacyStorePath)) {