AquaMail does not have user-created "local" folders (for POP3 or others).
Sorry, I am not using POP3 myself, so, my assumption was incorrect.
Off Topic: My inquisitive mind is curious if I understand correctly the behavior of Aquamail in the following scenario (an "edge case") for an IMAP account:
1. One of the "[functional]" automatic local folders ([Sent], [Drafts], [Deleted]) is "unlinked" from the corresponding one on the server, let's say, [Deleted].
2. A message is moved in Aquamail from Inbox to that folder.
3. If I understand Aquamail's behavior correctly, upon the next sync, the message in question will reappear in the Inbox in Aquamail.
4. The message is then deleted in Aquamail ("immediately delete"), which will delete the message on the server.
Is this correct?
If yes, then this would be a way (albeit very awkward) to preserve a message on the device while deleting it on the server.
PS. This would also be a scenario to topple down Aquamail and the entire phone by having (eventually) a huge database with very modest sync parameters.