Today Tampermonkey got corrupted again, and wondering if there was some way to debug this I loaded the extension folder with Load Unpacked and to my surprise Tampermonkey was back with all of the userscripts in place.
I know repair just wipes everything so maybe this is a better alternative for people to try out if the extension becomes corrupt.
I have no idea why this works, seems more like a Chromium bug than anything. Also not guaranteed to work I guess but I think true corruption of the database is pretty rare and most of these issues could possibly be fixed by this workaround.