diff --git a/src/agents/pi-embedded-runner/session-manager-init.ts b/src/agents/pi-embedded-runner/session-manager-init.ts
index 95c699947bd..b6b635004b5 100644
--- a/src/agents/pi-embedded-runner/session-manager-init.ts
+++ b/src/agents/pi-embedded-runner/session-manager-init.ts
@@ -12,6 +12,11 @@ type SessionMessageEntry = { type: "message"; message?: { role?: string } };
  *
  * This normalizes the file/session state so the first user prompt is persisted before the first
  * assistant entry, even for pre-created session files.
+ *
+ * NOTE: We only reset when there are no user messages yet (truly empty pre-created session).
+ * If user messages already exist, the session has real conversation history — an API error
+ * (e.g. 400/503) may have left the transcript without an assistant reply, but we must NOT
+ * wipe the history. The orphaned-user-message repair in attempt.ts handles that case instead.
  */
 export async function prepareSessionManagerForRun(params: {
   sessionManager: unknown;
@@ -33,6 +38,11 @@ export async function prepareSessionManagerForRun(params: {
   const hasAssistant = sm.fileEntries.some(
     (e) => e.type === "message" && (e as SessionMessageEntry).message?.role === "assistant",
   );
+  // A session with existing user messages has real conversation history (e.g. a prior turn that
+  // hit an API error). Do not reset it — the orphaned-user-message repair handles recovery.
+  const hasUser = sm.fileEntries.some(
+    (e) => e.type === "message" && (e as SessionMessageEntry).message?.role === "user",
+  );
 
   if (!params.hadSessionFile && header) {
     header.id = params.sessionId;
@@ -41,8 +51,9 @@ export async function prepareSessionManagerForRun(params: {
     return;
   }
 
-  if (params.hadSessionFile && header && !hasAssistant) {
+  if (params.hadSessionFile && header && !hasAssistant && !hasUser) {
     // Reset file so the first assistant flush includes header+user+assistant in order.
+    // Only applies to truly empty pre-created session files (no messages at all).
     await fs.writeFile(params.sessionFile, "", "utf-8");
     sm.fileEntries = [header];
     sm.byId?.clear?.();