First a description of what works:

In ED Pro 3.3 beta, in directory comparision, I can select a single empty directory whose status is "deleted" wrt. the other directory, and then right-click and choose "Copy to OTHER directory".
What does not work, is:
On simultaneously selecting two or more empty directories whose status is "deleted" wrt. the other dir, the contect menu option "Copy to OTHER directory" becomes grayed-out. Same is true for the appropriate symbol in the toolbar. Thus, cannot copy multiple empty dirs simultaneously to the other dir.
However, here is again something that works:
Additionally selecting a regular file to a set of simultaneously selected empty dirs (all of status "deleted" wrt. the other dir, don't know if that is relevant though), enables the "Copy to OTHER directory" content menu entry and toolbar symbol again.

Best,
Carsten