By refresh I mean sync, check mail, etc.
If you're in the account list and using context menus (long pressing the folder), then that has a Refresh item.
If you're in the folder itself, pull to refresh or Menu -> Refresh.
The scenario is then:
- The folder's current state is, say, 10 messages
- The server receives, say, 2 new messages in this folder, but those are not yet synced into Aqua
- You're doing Delete all -- Aqua deletes only those 10 messages -- and updates the counter to the now 2 remaining on the server
- At this point, if you do "refresh" you should see those two messages show.