Secondary drive failure, windows 10 errors

[Akuun]

So about a year ago I had a drive failure, fortunately it was my application drive

Unfortunately I didn't remedy this with a clean install of windows at the time

Now if I want to install an app that was previously installed (even a newer version), I have to find the registry entries and remove them first

Also the windows app manager shows apps to uninstall, but can't because nothing exists

Add to this the start menu entries that don't work

At this point doing a clean install would be days of backing up and reinstalling (yes I should back up regularly)

So is there any shortcut I can take?  (I've had issues with reg cleaners corrupting windows, so I would like to avoid if possible)