It's surely a bug introduced by inadequate "fix". Directory structure is the same kind of artifact as anything else, you should be able to archive whatever you want. In my case I have specific directory structure which is filled up based on several other jobs artifacts. After all automatic processes prepare delivery content we just fill up a few documents and HW test measurements done by hand and should be able to release that. The problem is that we either have to create a few empty directories (delivery won't pass with missing directories in structure) or remove placeholders created to let Jenkins archive those empty directories. You have powerful automation and yet you can't automate creating a few empty directories.
So yes, it's a bug. It does not behave as you would expect it to do and it took me too much time to discover that those directories are properly moved but not archived. Not even a log message telling that this thing won't be archived. I thought I messed up something and removed empty directories during delivery preparations. Great way of wasting time.