diff --git a/src/commands/doctor-state-integrity.test.ts b/src/commands/doctor-state-integrity.test.ts
index fddd53ebd72a..d9ae4b0f05ab 100644
--- a/src/commands/doctor-state-integrity.test.ts
+++ b/src/commands/doctor-state-integrity.test.ts
@@ -617,6 +617,10 @@ describe("doctor state integrity oauth dir checks", () => {
     const cfg: OpenClawConfig = {};
     setupSessionState(cfg, process.env, process.env.HOME ?? "");
     const storePath = resolveStorePath(cfg.session?.store, { agentId: "main" });
+    await upsertSessionEntry(
+      { agentId: "main", sessionKey: "agent:main:main", storePath },
+      { sessionId: "sqlite-main-session", updatedAt: Date.now() },
+    );
     await upsertSessionEntry(
       { agentId: "main", sessionKey: "agent:main:sqlite-only", storePath },
       { sessionId: "sqlite-only-session", updatedAt: Date.now() },
@@ -628,6 +632,7 @@ describe("doctor state integrity oauth dir checks", () => {
     });
 
     expect(stateIntegrityText()).not.toContain("recent sessions are missing transcripts");
+    expect(stateIntegrityText()).not.toContain("Main session transcript missing");
   });
 
   it("does not auto-archive orphan transcripts from non-interactive repair mode", async () => {
diff --git a/src/commands/doctor-state-integrity.ts b/src/commands/doctor-state-integrity.ts
index 46421882a6a3..45d9f42051ca 100644
--- a/src/commands/doctor-state-integrity.ts
+++ b/src/commands/doctor-state-integrity.ts
@@ -1474,7 +1474,9 @@ export async function noteStateIntegrity(
 
     const mainKey = resolveMainSessionKey(cfg);
     const mainEntry = store[mainKey];
-    if (mainEntry?.sessionId) {
+    // SQLite-owned transcripts live in the agent DB after import.
+    // Do not require the archived legacy JSONL for those sessions.
+    if (mainEntry?.sessionId && !sqliteSessionKeys.has(mainKey)) {
       const transcriptPath = resolveSessionFilePath(
         mainEntry.sessionId,
         mainEntry,