Deleting mail on the server when deleted from the phone is not really an AquaMail thing, it's more just the way POP3 works. Some email clients may have an option to sync/don't sync deletions with the server, but in my experience they're kinda iffy. Works with some services but not others.
There's some workarounds...
Don't ever empty the Deleted mailbox.
Keep email in the Inbox so you don't delete it by accident.
Move email in a desktop client to a safe Keepers or Important folder on the computer. It won't sync to the phone, but if email is deleted on the server you still have it available on the computer.
Or, from the FAQ:
How can I delete messages in AquaMail without deleting them from the server?
Each account has a setting for the default way to delete messages. The initial setting is “move to deleted first, delete from server when purging the deleted folder”.
To change the default: long press the account in the main screen and choose “Options and Folders”, then “Account options”.
Tap “Deleting messages” and choose “Hide in the app, keep on the server”.
This will change the default action icon for deleting messages from this account to “hide”.
Hidden messages can be restored by using the menu in the message list view. They will be also automatically deleted from the app at a later point to reclaim storage space.
Note that it’s not really necessary to delete messages from the app — old messages are automatically deleted over time without affecting the server, keeping storage usage under control. The default is to keep 250 most recent messages per folder (and can be changed in each account’s Folders and Options as “messages to keep”, renamed as “messages to cache” in 1.4).
Or, get rid of POP3. Convert the account to IMAP if possible.
Android since v1.0. Linux user since 2001.
