Removing a POP3 (or an IMAP, for that matter) account in AquaMail does not delete messages from the server.
Fair comment, but the only pop3 accounts I have ever had (by default) deleted messages from the server when downloaded.
I found this was the default but it could be changed. Indeed, I did change my iPhone behaviour so it left messages on the server, but the PC was still set to remove from server, so the only full copy was on the PC. Deleting the account in Thunderbird removed its folders and contents from the PC (for me it would have been the only full copy of 7 years' emails). Disabling the account left the messages in place on the pc, but never checked for email.
So I first disabled the accounts while I moved the messages received (and sent) during 7 years into the IMAP account and back onto the server.
As different providers or hosting services may have different defaults, it is at least an issue to watch for, but for most people these days maybe it is not an issue, as you will already have "leave on server" checked if you use webmail as well as a dedicated email client such as aquamail. I came to using email so long ago in the dial-up days, that 'download and remove from server' was the only practical solution.
Now, using IMAP on all platforms, I have my PC settings so that there should be two full copies of the messages. One on the server, one on the PC.