It would help me to know:
- What mail service this account is with (GoDaddy, Gmail, Yahoo etc)
- Whether the Deleted folder in Aqua is set to sync with the server. You can tell two ways: 1) if there is a color triangle to the left of Deleted in the account list 2) long press Deleted, check if the top item in the popup menu says "-> ServerFolderNameHere"
If the folder is not set to sync with the server, please do this:
- Long press the account -> options and folders -> folders -> find the server side Deleted folder (Trash, Trash Can, Deleted Items, Bin, etc.), tap it, choose "Sync with Deleted".
If the folder *is* set to sync, please use web mail to check whether Aqua moves your messages on the server.
If it is, then the issue is with your desktop mail app's configuration.
If Aqua is not moving messages to Deleted in web mail, then please create a debug log, with "raw data", as described below.