diff --git a/src/auto-reply/reply/agent-runner.heartbeat-typing.runreplyagent-typing-heartbeat.retries-after-compaction-failure-by-resetting-session.test.ts b/src/auto-reply/reply/agent-runner.heartbeat-typing.runreplyagent-typing-heartbeat.retries-after-compaction-failure-by-resetting-session.test.ts
index 6978f88fc..f583daf6a 100644
--- a/src/auto-reply/reply/agent-runner.heartbeat-typing.runreplyagent-typing-heartbeat.retries-after-compaction-failure-by-resetting-session.test.ts
+++ b/src/auto-reply/reply/agent-runner.heartbeat-typing.runreplyagent-typing-heartbeat.retries-after-compaction-failure-by-resetting-session.test.ts
@@ -3,6 +3,7 @@ import { tmpdir } from "node:os";
 import path from "node:path";
 import { describe, expect, it, vi } from "vitest";
 import type { SessionEntry } from "../../config/sessions.js";
+import * as sessions from "../../config/sessions.js";
 import type { TypingMode } from "../../config/types.js";
 import type { TemplateContext } from "../templating.js";
 import type { GetReplyOptions } from "../types.js";
@@ -127,11 +128,14 @@ describe("runReplyAgent typing (heartbeat)", () => {
     try {
       const sessionId = "session";
       const storePath = path.join(stateDir, "sessions", "sessions.json");
-      const sessionEntry = { sessionId, updatedAt: Date.now() };
+      const transcriptPath = sessions.resolveSessionTranscriptPath(sessionId);
+      const sessionEntry = { sessionId, updatedAt: Date.now(), sessionFile: transcriptPath };
       const sessionStore = { main: sessionEntry };
 
       await fs.mkdir(path.dirname(storePath), { recursive: true });
       await fs.writeFile(storePath, JSON.stringify(sessionStore), "utf-8");
+      await fs.mkdir(path.dirname(transcriptPath), { recursive: true });
+      await fs.writeFile(transcriptPath, "ok", "utf-8");
 
       runEmbeddedPiAgentMock
         .mockImplementationOnce(async () => {
@@ -175,11 +179,14 @@ describe("runReplyAgent typing (heartbeat)", () => {
     try {
       const sessionId = "session";
       const storePath = path.join(stateDir, "sessions", "sessions.json");
-      const sessionEntry = { sessionId, updatedAt: Date.now() };
+      const transcriptPath = sessions.resolveSessionTranscriptPath(sessionId);
+      const sessionEntry = { sessionId, updatedAt: Date.now(), sessionFile: transcriptPath };
       const sessionStore = { main: sessionEntry };
 
       await fs.mkdir(path.dirname(storePath), { recursive: true });
       await fs.writeFile(storePath, JSON.stringify(sessionStore), "utf-8");
+      await fs.mkdir(path.dirname(transcriptPath), { recursive: true });
+      await fs.writeFile(transcriptPath, "ok", "utf-8");
 
       runEmbeddedPiAgentMock
         .mockImplementationOnce(async () => ({
@@ -229,11 +236,14 @@ describe("runReplyAgent typing (heartbeat)", () => {
     try {
       const sessionId = "session";
       const storePath = path.join(stateDir, "sessions", "sessions.json");
-      const sessionEntry = { sessionId, updatedAt: Date.now() };
+      const transcriptPath = sessions.resolveSessionTranscriptPath(sessionId);
+      const sessionEntry = { sessionId, updatedAt: Date.now(), sessionFile: transcriptPath };
       const sessionStore = { main: sessionEntry };
 
       await fs.mkdir(path.dirname(storePath), { recursive: true });
       await fs.writeFile(storePath, JSON.stringify(sessionStore), "utf-8");
+      await fs.mkdir(path.dirname(transcriptPath), { recursive: true });
+      await fs.writeFile(transcriptPath, "ok", "utf-8");
 
       runEmbeddedPiAgentMock.mockImplementationOnce(async () => ({
         payloads: [{ text: "Message ordering conflict - please try again.", isError: true }],
@@ -260,6 +270,7 @@ describe("runReplyAgent typing (heartbeat)", () => {
       });
       expect(payload.text?.toLowerCase()).toContain("reset");
       expect(sessionStore.main.sessionId).not.toBe(sessionId);
+      await expect(fs.access(transcriptPath)).rejects.toBeDefined();
 
       const persisted = JSON.parse(await fs.readFile(storePath, "utf-8"));
       expect(persisted.main.sessionId).toBe(sessionStore.main.sessionId);
diff --git a/src/auto-reply/reply/agent-runner.ts b/src/auto-reply/reply/agent-runner.ts
index 215756967..42ca85111 100644
--- a/src/auto-reply/reply/agent-runner.ts
+++ b/src/auto-reply/reply/agent-runner.ts
@@ -1,4 +1,5 @@
 import crypto from "node:crypto";
+import fs from "node:fs";
 import { setCliSessionId } from "../../agents/cli-session.js";
 import { lookupContextTokens } from "../../agents/context.js";
 import { DEFAULT_CONTEXT_TOKENS } from "../../agents/defaults.js";
@@ -8,6 +9,7 @@ import { queueEmbeddedPiMessage } from "../../agents/pi-embedded.js";
 import { hasNonzeroUsage } from "../../agents/usage.js";
 import {
   resolveAgentIdFromSessionKey,
+  resolveSessionFilePath,
   resolveSessionTranscriptPath,
   type SessionEntry,
   updateSessionStore,
@@ -247,6 +249,8 @@ export async function runReplyAgent(params: {
   };
   const resetSessionAfterRoleOrderingConflict = async (reason: string): Promise<boolean> => {
     if (!sessionKey || !activeSessionStore || !storePath) return false;
+    const prevEntry = activeSessionStore[sessionKey] ?? activeSessionEntry;
+    const prevSessionId = prevEntry?.sessionId;
     const nextSessionId = crypto.randomUUID();
     const nextEntry: SessionEntry = {
       ...(activeSessionStore[sessionKey] ?? activeSessionEntry),
@@ -279,6 +283,19 @@ export async function runReplyAgent(params: {
     defaultRuntime.error(
       `Role ordering conflict (${reason}). Restarting session ${sessionKey} -> ${nextSessionId}.`,
     );
+    if (prevSessionId) {
+      const transcriptCandidates = new Set<string>();
+      const resolved = resolveSessionFilePath(prevSessionId, prevEntry, { agentId });
+      if (resolved) transcriptCandidates.add(resolved);
+      transcriptCandidates.add(resolveSessionTranscriptPath(prevSessionId, agentId));
+      for (const candidate of transcriptCandidates) {
+        try {
+          fs.unlinkSync(candidate);
+        } catch {
+          // Best-effort cleanup.
+        }
+      }
+    }
     return true;
   };
   try {