[pkscout]

Strange.  If I set the destination of the AIF on my NAS, then AS does not delete empty folders after they are created.

I'd need to see a full debug log, but that potentially points to either a permissions issue or maybe an issue with Kodi's virtual file system (which is the thing that interfaces between Kodi and the actual mounts).

Strange.  I tried it on my Win10 PC and it worked normally.  It just has problems on my RPi 3B+.

Here is the log.

That certainly points to some kind of configuration difference on the RPi.  I noticed you are using SMB.  You might check to make sure both instances of Kodi are using the same SMB version when connecting.

https://kodi.wiki/view/Settings/Services/SMB_Client