diff --git a/src/common/inlineScript/cacheLayout.ts b/src/common/inlineScript/cacheLayout.ts
index 71f125d4..7554ed08 100644
--- a/src/common/inlineScript/cacheLayout.ts
+++ b/src/common/inlineScript/cacheLayout.ts
@@ -151,10 +151,13 @@ export async function restoreMetaJsonBackupUnderLock(
     }
 
     const validBackups: Array<{ readonly path: string; readonly metadata: InlineScriptEnvMeta }> = [];
+    let hasUnsupportedBackup = false;
     for (const entry of entries.filter((name) => META_JSON_BACKUP_FILENAME_RE.test(name))) {
         const result = await inspectMetaJsonFile(path.join(envDir.fsPath, entry));
         if (result.kind === 'valid' && isCompatible(result.metadata)) {
             validBackups.push({ path: path.join(envDir.fsPath, entry), metadata: result.metadata });
+        } else if (result.kind === 'unsupported') {
+            hasUnsupportedBackup = true;
         } else if (result.kind === 'unavailable' || result.kind === 'missing') {
             // A listed candidate changing or becoming unreadable is an
             // uncertain scan; preserve the entry rather than rebuilding it.
@@ -163,7 +166,7 @@ export async function restoreMetaJsonBackupUnderLock(
     }
 
     if (validBackups.length === 0) {
-        return { kind: 'missing' };
+        return { kind: hasUnsupportedBackup ? 'unsupported' : 'missing' };
     }
 
     // `lastUsedAt` is schema-validated canonical ISO text. Prefer the newest
diff --git a/src/features/envManagers.ts b/src/features/envManagers.ts
index a99198e4..b8639ada 100644
--- a/src/features/envManagers.ts
+++ b/src/features/envManagers.ts
@@ -18,6 +18,7 @@ import {
 import {
     InlineScriptRouteabilityChangeEvent,
     InlineScriptRoutingRegistry,
+    getInlineScriptRoutingKey,
 } from '../common/inlineScript/routingRegistry';
 import { traceError, traceVerbose } from '../common/logging';
 import { StopWatch } from '../common/stopWatch';
@@ -420,19 +421,29 @@ export class PythonEnvironmentManagers implements EnvironmentManagers {
         }
 
         if (scope instanceof Uri) {
-            this.updateInlineRoutingOverride(scope, manager, environment);
-            this.clearInlineActiveSelection(scope, manager, inlineClearOperation);
             if (
-                clearingInlineRoutingOverride &&
-                (await this.publishEffectiveEnvironmentAfterOverrideClear(
+                this.commitInlineRoutingOperation(
                     scope,
                     manager,
-                    key,
                     operation,
+                    inlineClearOperation,
                     inlineOverrideHandoffOperation,
-                ))
+                )
             ) {
-                return;
+                this.updateInlineRoutingOverride(scope, manager, environment);
+                this.clearInlineActiveSelection(scope, manager, inlineOverrideHandoffOperation ?? inlineClearOperation);
+                if (
+                    clearingInlineRoutingOverride &&
+                    (await this.publishEffectiveEnvironmentAfterOverrideClear(
+                        scope,
+                        manager,
+                        key,
+                        operation,
+                        inlineOverrideHandoffOperation,
+                    ))
+                ) {
+                    return;
+                }
             }
         }
         if (!publishInlineSelection) {
@@ -511,8 +522,20 @@ export class PythonEnvironmentManagers implements EnvironmentManagers {
                     await setAllManagerSettings(settings);
                 }
                 selections.forEach((selection) => {
-                    this.updateInlineRoutingOverride(selection.scope, manager, environment);
-                    this.clearInlineActiveSelection(selection.scope, manager, selection.inlineClearOperation);
+                    // Only a current (non-superseded) PEP 723 routing operation may mutate the
+                    // per-script override; the ordinary project/global selection lane below is
+                    // committed independently so a stale inline op cannot suppress it.
+                    if (
+                        this.commitInlineRoutingOperation(
+                            selection.scope,
+                            manager,
+                            selection.operation,
+                            selection.inlineClearOperation,
+                        )
+                    ) {
+                        this.updateInlineRoutingOverride(selection.scope, manager, environment);
+                        this.clearInlineActiveSelection(selection.scope, manager, selection.inlineClearOperation);
+                    }
                     if (!selection.publishInlineSelection) {
                         return;
                     }
@@ -932,6 +955,28 @@ export class PythonEnvironmentManagers implements EnvironmentManagers {
         }
     }
 
+    private commitInlineRoutingOperation(
+        scope: Uri,
+        manager: InternalEnvironmentManager,
+        selectionOperation: number,
+        inlineClearOperation?: number,
+        inlineOverrideHandoffOperation?: number,
+    ): boolean {
+        // Gate strictly to the manually enabled PEP 723 routing feature and to file .py scopes.
+        // For the feature-off or non-script case, proceed exactly as before.
+        if (!this.inlineScriptRouting || getInlineScriptRoutingKey(scope) === undefined) {
+            return true;
+        }
+        const operation =
+            manager.id === INLINE_SCRIPT_MANAGER_ID
+                ? selectionOperation
+                : (inlineOverrideHandoffOperation ?? inlineClearOperation);
+        return (
+            operation === undefined ||
+            this.commitSelectionOperation(this.getInlineScriptSelectionKey(scope), operation)
+        );
+    }
+
     private canPersistManagerSettingForScope(
         scope: Uri,
         manager: InternalEnvironmentManager,
diff --git a/src/test/common/inlineScript/cacheLayout.unit.test.ts b/src/test/common/inlineScript/cacheLayout.unit.test.ts
index 57c93084..53815837 100644
--- a/src/test/common/inlineScript/cacheLayout.unit.test.ts
+++ b/src/test/common/inlineScript/cacheLayout.unit.test.ts
@@ -330,18 +330,29 @@ suite('inlineScriptCacheLayout', () => {
             assert.strictEqual(await fs.pathExists(getMetaJsonPath(envDir).fsPath), false);
         });
 
-        test('rejects temp, malformed, unsupported, and oversized artifacts without restoring them', async () => {
+        test('rejects temp, malformed, and oversized artifacts without restoring them', async () => {
             const finalPath = getMetaJsonPath(envDir).fsPath;
             await fs.writeFile(`${finalPath}.tmp-abcdef123456`, JSON.stringify(makeMeta()));
             await fs.writeFile(`${finalPath}.backup-ABCDEF123456`, JSON.stringify(makeMeta()));
             await writeBackup('111111111111', 'not json');
-            await writeBackup('222222222222', JSON.stringify({ ...makeMeta(), schemaVersion: 99 }));
             await writeBackup('333333333333', Buffer.alloc(1024 * 1024 + 1, 0x20));
 
             assert.deepStrictEqual(await restoreMetaJsonBackupUnderLock(envDir), { kind: 'missing' });
             assert.strictEqual(await fs.pathExists(finalPath), false);
         });
 
+        test('preserves a future-schema backup as unsupported when the primary is absent', async () => {
+            const finalPath = getMetaJsonPath(envDir).fsPath;
+            const backup = backupPath('222222222222');
+            await writeBackup('111111111111', 'not json');
+            await writeBackup('222222222222', JSON.stringify({ ...makeMeta(), schemaVersion: 99 }));
+            await writeBackup('333333333333', Buffer.alloc(1024 * 1024 + 1, 0x20));
+
+            assert.deepStrictEqual(await restoreMetaJsonBackupUnderLock(envDir), { kind: 'unsupported' });
+            assert.strictEqual(await fs.pathExists(finalPath), false);
+            assert.strictEqual(await fs.pathExists(backup), true);
+        });
+
         test('rejects a symlink backup without restoring it', async function () {
             const externalPath = path.join(tmpDir, 'external-meta.json');
             await fs.writeFile(externalPath, JSON.stringify(makeMeta()));
diff --git a/src/test/features/envManagers.lastKnown.unit.test.ts b/src/test/features/envManagers.lastKnown.unit.test.ts
index 38f416c8..a91d8e43 100644
--- a/src/test/features/envManagers.lastKnown.unit.test.ts
+++ b/src/test/features/envManagers.lastKnown.unit.test.ts
@@ -299,6 +299,145 @@ suite('PythonEnvironmentManagers getLastKnownEnvironment', () => {
         assert.deepStrictEqual(events.map((event) => event.new), [second]);
     });
 
+    test('does not let an older non-inline selection install an override after a newer inline selection', async () => {
+        const script = Uri.file('/workspace/project/script.py');
+        projectsByUri.set(script.toString(), { name: 'project', uri: Uri.file('/workspace/project') });
+        let releaseOlderSelection: (() => void) | undefined;
+        let signalOlderSelection: (() => void) | undefined;
+        const olderSelectionStarted = new Promise<void>((resolve) => {
+            signalOlderSelection = resolve;
+        });
+        const olderSelectionGate = new Promise<void>((resolve) => {
+            releaseOlderSelection = resolve;
+        });
+        const selectedSet = sinon.stub().callsFake(async () => {
+            signalOlderSelection!();
+            await olderSelectionGate;
+        });
+        let selectedEnvironment: PythonEnvironment;
+        const selectedId = registerManager(async () => selectedEnvironment, selectedSet, 'venv');
+        let inlineEnvironment: PythonEnvironment;
+        const inlineId = registerManager(async () => inlineEnvironment, async () => undefined, 'inline-script');
+        selectedEnvironment = {
+            ...makeEnv('selected'),
+            envId: { id: 'selected', managerId: selectedId },
+        };
+        inlineEnvironment = {
+            ...makeEnv('inline'),
+            envId: { id: 'inline', managerId: inlineId },
+        };
+        defaultManagerId = selectedId;
+        markInlineScript(script);
+        const events: DidChangeEnvironmentEventArgs[] = [];
+        envManagers.onDidChangeActiveEnvironment((event) => events.push(event));
+
+        const olderSelection = envManagers.setEnvironment(script, selectedEnvironment, false);
+        await olderSelectionStarted;
+        await envManagers.setEnvironment(script, inlineEnvironment, false);
+        releaseOlderSelection!();
+        await olderSelection;
+
+        // The stale non-inline selection must not hijack the script's PEP 723 routing…
+        assert.strictEqual(envManagers.getEnvironmentManager(script)?.id, inlineId);
+        assert.strictEqual(envManagers.getLastKnownEnvironment(script), inlineEnvironment);
+        assert.ok(events.some((event) => event.new === inlineEnvironment));
+        // …but its ordinary containing-project selection lane is independent and is not suppressed.
+        assert.ok(events.some((event) => event.new === selectedEnvironment));
+    });
+
+    test('does not let an older batch inline selection clear a newer non-inline override', async () => {
+        const script = Uri.file('/workspace/project/script.py');
+        projectsByUri.set(script.toString(), { name: 'project', uri: Uri.file('/workspace/project') });
+        let releaseOlderBatch: (() => void) | undefined;
+        let signalOlderBatch: (() => void) | undefined;
+        const olderBatchStarted = new Promise<void>((resolve) => {
+            signalOlderBatch = resolve;
+        });
+        const olderBatchGate = new Promise<void>((resolve) => {
+            releaseOlderBatch = resolve;
+        });
+        let selectedEnvironment: PythonEnvironment;
+        const selectedId = registerManager(async () => selectedEnvironment, async () => undefined, 'venv');
+        const inlineSet = sinon.stub().callsFake(async () => {
+            signalOlderBatch!();
+            await olderBatchGate;
+        });
+        let inlineEnvironment: PythonEnvironment;
+        const inlineId = registerManager(async () => inlineEnvironment, inlineSet, 'inline-script');
+        selectedEnvironment = {
+            ...makeEnv('selected'),
+            envId: { id: 'selected', managerId: selectedId },
+        };
+        inlineEnvironment = {
+            ...makeEnv('inline'),
+            envId: { id: 'inline', managerId: inlineId },
+        };
+        defaultManagerId = selectedId;
+        markInlineScript(script);
+        const events: DidChangeEnvironmentEventArgs[] = [];
+        envManagers.onDidChangeActiveEnvironment((event) => events.push(event));
+
+        const olderBatch = envManagers.setEnvironments([script], inlineEnvironment, false);
+        await olderBatchStarted;
+        await envManagers.setEnvironment(script, selectedEnvironment, false);
+        const eventsAfterNewerSelection = [...events];
+        releaseOlderBatch!();
+        await olderBatch;
+
+        assert.strictEqual(envManagers.getEnvironmentManager(script)?.id, selectedId);
+        assert.strictEqual(envManagers.getLastKnownEnvironment(script), selectedEnvironment);
+        assert.deepStrictEqual(events, eventsAfterNewerSelection);
+    });
+
+    test('routes each same-project script to its own override in a batch non-inline selection', async () => {
+        const project = { name: 'project', uri: Uri.file('/workspace/project') };
+        const firstScript = Uri.file('/workspace/project/first.py');
+        const secondScript = Uri.file('/workspace/project/second.py');
+        projectsByUri.set(firstScript.toString(), project);
+        projectsByUri.set(secondScript.toString(), project);
+        let selectedEnvironment: PythonEnvironment;
+        const selectedId = registerManager(async () => selectedEnvironment, async () => undefined, 'venv');
+        registerManager(async () => undefined, async () => undefined, 'inline-script');
+        selectedEnvironment = { ...makeEnv('selected'), envId: { id: 'selected', managerId: selectedId } };
+        markInlineScript(firstScript);
+        markInlineScript(secondScript);
+
+        await envManagers.setEnvironments([firstScript, secondScript], selectedEnvironment, false);
+
+        // Each script commits on its own per-file inline key, so the shared containing-project
+        // revision cannot make the first script skip installing its routing override.
+        assert.strictEqual(envManagers.getEnvironmentManager(firstScript)?.id, selectedId);
+        assert.strictEqual(envManagers.getEnvironmentManager(secondScript)?.id, selectedId);
+    });
+
+    test('applies a normal non-inline batch across distinct projects without a routing registry', async () => {
+        recreateEnvManagersWithoutRouting();
+        const projectOne = { name: 'one', uri: Uri.file('/workspace/one') };
+        const projectTwo = { name: 'two', uri: Uri.file('/workspace/two') };
+        projectsByUri.set(projectOne.uri.toString(), projectOne);
+        projectsByUri.set(projectTwo.uri.toString(), projectTwo);
+        const managerSet = sinon.stub().resolves();
+        let selectedEnvironment: PythonEnvironment;
+        const managerId = registerManager(async () => selectedEnvironment, managerSet, 'venv');
+        selectedEnvironment = { ...makeEnv('selected'), envId: { id: 'selected', managerId } };
+        const settings = sinon.stub(settingHelpers, 'setAllManagerSettings').resolves();
+        const events: DidChangeEnvironmentEventArgs[] = [];
+        envManagers.onDidChangeActiveEnvironment((event) => events.push(event));
+
+        await envManagers.setEnvironments([projectOne.uri, projectTwo.uri], selectedEnvironment);
+
+        assert.strictEqual(managerSet.callCount, 1);
+        assert.deepStrictEqual(managerSet.firstCall.args[0], [projectOne.uri, projectTwo.uri]);
+        assert.strictEqual(envManagers.getLastKnownEnvironment(projectOne.uri), selectedEnvironment);
+        assert.strictEqual(envManagers.getLastKnownEnvironment(projectTwo.uri), selectedEnvironment);
+        assert.deepStrictEqual(
+            events.map((event) => event.new),
+            [selectedEnvironment, selectedEnvironment],
+        );
+        assert.strictEqual(settings.callCount, 1);
+        assert.strictEqual(settings.firstCall.args[0].length, 2);
+    });
+
     test('publishes inline environments with the same ID at different paths', async () => {
         const scope = Uri.file('/workspace/script.py');
         const managerId = registerManager(async () => undefined, async () => undefined, 'inline-script');