Remove All deletes all programs, settings, and files, and leaves you with a fresh, activated install of Windows (no, it does not delete Windows itself).
I'd suggest the "keep files" option, as this will only remove programs and settings, and leave your user account and files intact. Basically like having a fresh install, but all your files are already there.
This option also doesn't fully delete programs and settings, just moves them into C:\Windows.old. So if you want to recover anything from there (like your browser profile, Steam/Origin folders, etc.) you can do that and then delete the rest with Disk Cleanup.