Other than repository folders, you can rename any folder (provided the new name was not used for another sibling folder)
Why repository folders should not be renamed is because the Deploy keys that are used the system to give you Git permissions would be based on the older folder-name.
Important
You can rename a sub-folder within a repository. If you do that, first make sure that the rest of the members working on that same repository are currently NOT working on that folder. Then do a commit and push of the repository after your renamed it.