Tried to reply on Youtube but it keeps deleting my comment, of course, so apologies for going off topic here.
I've had that issue with Git and Autoload paths getting "lost" due to case sensitivity shenanigans. TL;DR : check that files are named in snake_case on all devices
By default, Git does not consider filenames to be case-sensitive. If you commit Test.txt, then rename it to test.txt, the name change is not tracked, even though changes to the content of the file will be. In Git it will look like you both have the same files, though in reality there is a case discrepancy in your filenames, which eventually messes up the Autoload.
On top of that, some OSes are case-insensitive (Windows), others are not (Linux), so you're more prone to running into these kind of issues if your team uses different OSes. The Godot doc also warns you that exporting a project that runs perfectly on Windows might fail to run on Linux due to this, which is why it advises to keep files and folder names in snake_case.
If it happens again, you can use an intermediate commit (Test.txt > test_wip.txt > test.txt) to force Git to track the change. There's supposedly also a way to configure Git to be case-sensitive, though I haven't tried.
Finally, since you mentioned UID corruption (which can def happen), there's a very handy feature in Godot : Project > Tools > Upgrade project files. This regenerates the UID cache and re-saves all your scenes, which can solve many issues without going nuclear and re-cloning the whole project. :)