Im pretty sure there is currently no proper way to do this so i guess you can consider this a feature request.
Example Scenario: You create a new share and forget to setup disk assignment, or you have an empty share and you want to move it to a different disk.
In ether case a new folder will be created on the assigned disk(s) and an empty folder will be left on the previous disk(s) and as far as i can tell there is not proper way to remove these empty folders.
The only way i know of to remove this empty folder is to manually delete it from the disk then run a parity check to correct the error that causes. This is far from an ideal solution. It would be nice if unraid had the ability to clean up empty share folders in a way that does not break parity.
If there is already way to do this then i apologies but i could not find anything related to this on the forum or google.