Even with the "Are you sure" dialog (already there, and on by default), people still manage to delete important messages...
...and then contact me ("Help, I've lost my Kennedy assassination photos... not that Oswald guy, the other ones...")
Why go to all this trouble of deleting messages when the app has automatic nightly housekeeping, and keeps only 250 most recent ones on the device?
For your everyday (every-evening) transition, just long press the folder (while still in the account list) and mark as read all messages received during the day.
And then, if your PC is a permanent repository, is your PC mail set to delete all messages from the server after it checks mail? If so, set the account in AquaMail to remove deleted messages, or "purge when empty", and it will delete those old messages automatically (from the device only). Those options are under the per-account Options and Folders (long press the account to open), then look in Account options or POP3 options.