diff --git a/src/main/codex/config-settings-baseline-v3.test.ts b/src/main/codex/config-settings-baseline-v3.test.ts
index 78aba051fad..85ef6bf7a54 100644
--- a/src/main/codex/config-settings-baseline-v3.test.ts
+++ b/src/main/codex/config-settings-baseline-v3.test.ts
@@ -142,6 +142,29 @@ describe('Codex settings baseline v3 persistence', () => {
     expect(readCodexSettingsBaseline(runtimeHomePath)).not.toBeNull()
   })
 
+  it('writes v2 when ordinary tracking is requested without source authority', () => {
+    writeCodexSettingsBaseline(runtimeHomePath, {
+      settings: new Map([
+        ['model', '"gpt-5"'],
+        ['personality', '"local"']
+      ]),
+      conflicts: new Map(),
+      knownPromotedKeys: new Set(['model']),
+      sourceIsAuthoritative: false,
+      tracksAllOrdinarySettings: true
+    })
+
+    expect(readStoredBaseline()).toMatchObject({
+      version: 2,
+      settings: { model: '"gpt-5"', personality: '"local"' }
+    })
+    expect(readStoredBaseline().sourceAuthority).toBeUndefined()
+    expect(readCodexSettingsBaseline(runtimeHomePath)).toMatchObject({
+      tracksAllOrdinarySettings: false,
+      sourceIsAuthoritative: false
+    })
+  })
+
   it('keeps promoted ancestors when an unlisted value forces v2 fallback', () => {
     const settings = new Map<string, string | null>([
       ['model', '"gpt-5"'],
diff --git a/src/main/codex/config-settings-baseline.ts b/src/main/codex/config-settings-baseline.ts
index 88f039b7b4e..2451212bb5e 100644
--- a/src/main/codex/config-settings-baseline.ts
+++ b/src/main/codex/config-settings-baseline.ts
@@ -197,7 +197,9 @@ function isCodexSettingsConflict(value: unknown): value is CodexSettingsConflict
 
 function buildStoredSettingsBaseline(baseline: CodexSettingsBaseline): StoredSettingsBaseline {
   const preferred: StoredSettingsBaseline = {
-    version: baseline.tracksAllOrdinarySettings ? 3 : 2,
+    // A complete ordinary-key snapshot is only authoritative when it came
+    // from a readable system mirror; otherwise v2 keeps absence ambiguous.
+    version: baseline.tracksAllOrdinarySettings && baseline.sourceIsAuthoritative ? 3 : 2,
     settings: Object.fromEntries(baseline.settings)
   }
   if (baseline.conflicts.size > 0) {