If Microsoft OneDrive decides to mess with the Cryptomator folder I created and just delete the folder, would that mess anything up with Cryptomator, like uploading or being able to view my files?
Is there anything I could do to prevent OneDrive from even touching that folder at all?
Onedrive will not change your files or folder structure by itself. This would be a huge issue and I never heard about this.
A messed up vault structure will destroy your vault.
There’s no function to write protect a folder in onedrive. And even if there would be, you would not be able to run a cryptomator vault in such a folder. Because you want your onedrive client to sync changes with your local drive (means the local cryptomator vault files)