I have my client configured for delete from server and I find that when I delete an email and try to read another email that hasn't fully loaded from the server, I get an error that that email isn't on the server.
If I wait several minutes, it loads the email without error.
I'm not sure if this is an issue with my ISP's mail server or the aquamail client. I haven't experienced it on any other mail client, though.
The account is POP3.