I did that last night after deleting the emails, but have just done it again - no change in Mail D & D usage.
I should confess that I understand very little about how email accounts should be managed, and I suspect that I have done things in problematic ways. For instance, I have 2 email accounts on the iPad. One is the default Comcast account which I use almost exclusively, and the other is an iCloud account (@me.com). When I erased emails last evening, I did so in all mailboxes in both accounts. I suspect the iCloud account may be a key to this puzzle.