sorry, I cant really say without seeing the computer...
copying files, should work with Git , as its a file based system... nothing 'hidden' going on. but its not really the correct 'workflow', so its possible to get yourself in a mess... but because its not the 'right' way to do thing, to sort it out, you need to have a bit more git knowledge to know what is wrong.
one thing, if you are trying to transfer the repo from one computer to another, you have to make sure you take the hidden files as well (which reside in a .git directory)
also i seem to remember, it has to be in the same directory, as it was before.
if you start copying files then you must only then sync from the new computer, and on the old computer to a delete lib, to resync.... to ensure you are not accidentally changing files on two computers.
though seriously, id not start messing with this if you don't understand how git works.
.. this is why the Axoloti UI only supports a concept of syncing, to keep these complications away from users.
the intended workflow would be you sync the old computer to the cloud, then download the work to the new computer by sync from the cloud.
if this doesn't work, I suggest people delete library and resync...
what i would do if i were you is quite simple...
move the folder with the offending conflicts somewhere else on your drive.
sync from the cloud, then check the files that had the conflict, to see if you want the one from the cloud, or the backup directory you just created.
p.s. all the above is not a limitation of git, thousands of programmers do simultaneous changes to files every day, but they know about version control systems, and how to merge changes, and also prevent conflicts... also they can edit the underlying files directly. (e.g. the equivalent of editing a axo file with a text editor) ... these are all things we do not want to get into with Axoloti.