If by "listed in the account" you mean the number in the app's main window -- then see @Paris Geek's answer (he's a world-famous expert on AquaMail, and I really mean it).
For comparison, my Gmail account has over 100K messages in some folders, and the app only keeps the most recent 25 up to date on the device (enough for my needs).
That's fine, that's how Aqua is designed to work -- download only a limited number of most recent messages.
