PC Master Race

Lol, while Git does a shit ton more than just file syncing, you're effectively complaining that mixing two methods of syncing files causes problems.

I feel like that's kind of obvious that it would be a bad idea.

Also, how in the hell are you using Git that it could even be possible to lose thousands of hours of work? Sounds like you guy weren't properly checking in/out code and using branches well. There shouldn't be that much work put in between sending it back to the repo on the server. Make a branch, check in every few hours even if it's not compiling or finished. When it's finally done you can use the end result. No need to make big "complete" commits when you can just shove all the messy in progress ones into a branch and merge the whole thing when it's done and ready.

As far as OneDrive arbitrarily taking over folders? That should never happen. I'm not aware of a configuration that would make that possible (not saying there isn't one, just that you'd have to go looking for it if you really wanted to fuck this up like that).

The normal setting is for it to sync the Documents, Pictures, and Desktop folders (including any sub files and folders recursively). So just store your repos outside of those folders and you shouldn't have any problems.

To be fair, I've also seen OneDrive cause problems with PowerShell modules installed under the user (the default install location when using Install-Module). That tosses them in a subfolder under Documents, and "download files on demand" doesn't mix well with "load this entire code library of multiple files". So either use a custom install path, or install on your machine in the AllUsers scope (putting them in the Progams folder I believe).