Trouble With Running An Inplace Upgrade For Windows 11 Using Media Creation Tool

Title: Troubleshooting In-Place Upgrade for Windows 11 Using Media Creation Tool

Introduction

Upgrading your Windows 11 installation can sometimes be a complex process, especially when system issues arise. If you’re experiencing difficulties with an in-place upgrade—such as system instability or corrupted applications—it’s critical to approach the process carefully to preserve your data. This guide discusses common issues faced during in-place upgrades and provides practical solutions to help you navigate these challenges effectively.

Understanding the Problem

Many users encounter problems when their Windows 11 environment becomes unstable after installing problematic software or making unintended changes. For example, running certain programs may inadvertently corrupt or delete essential system folders, such as the WindowsApps directory, which manages Windows Store applications. Such issues can render core functionalities—including the Windows Store and even system utilities like Windows Terminal—inoperable.

In this scenario, the user reports that after running an unwelcome program, all Windows Store apps ceased to function, and critical system components failed to operate correctly. Attempting to perform an in-place upgrade via the Media Creation Tool (MCT) results in difficulties, specifically with the “Choose what to keep” screen acting unpredictably—flickering briefly and then skipping, which prevents proper customization of the upgrade process.

Challenges During Upgrade

One common obstacle during in-place upgrades is system corruption caused by missing or modified system files. When core folders like WindowsApps are deleted or altered, the system’s ability to locate required executable files (.exe) diminishes. This can lead to failures in launching Windows Store apps and other system utilities, including command-line tools like Windows Terminal.

Specifically, if the upgrade process cannot correctly identify system files or if the upgrade wizard skips essential steps, users may find themselves unable to retain existing files, settings, or apps easily. Additionally, issues like the “Choose what to keep” screen flashing and skipping suggest underlying system inconsistencies that need addressing before a successful upgrade.

Recommended Solutions

1. Backup Important Data: Before attempting further system modifications, ensure all critical files are backed up to avoid data loss.

2. Run System File Checker (SFC) and DISM:

3. Open Command Prompt as Administrator.
4. Run sfc /scannow to repair corrupted system files.
5. Follow with DISM /Online /Cleanup-Image /RestoreHealth to fix component store corruption.

6. Restart your PC and verify if system issues are resolved.

7. Restore Missing System Folders: