If you’re really having “issues” with your Windows installation, the best thing to do is to do format and clean install of Windows. With things like OneDrive’s known folder move (where your Documents, Desktop and Pictures folders are automatically synced), it’s fairly painless to start from scratch. Obviously you’re still going to have to reinstall your GPU drivers and MSFS2020.
At work, I use the Windows ADK to prepare Windows system images with pre-loaded Office and other common software, etc. It takes me about 15 minutes to boot from an external SSD and lay down a clean Windows image onto my computer.