I am having the same problem as described in this thread.
I have just migrated to Kopano and in Zarafa’s gateway.cfg I had imap_expunge_on_delete = yes.
I also have this in Kopano’s gateway.cfg, but to no avail.
I also tried with mail.imap.expunge_after_delete = true in Thunderbird’s configuration.
I can see expunge commands being sent if I trace communication with WireShark.