I can only confirm what has already been said -- Aqua does not delete messages from the server when it checks mail.
It only does this when the user wants it to -- for a POP3 account, this means moving to deleted first, then purging the deleted folder. Or if you do Menu -> Delete immediately on a message (bypassing the Deleted folder).
Not going to question what you're seeing... anything is possible, but I'm as sure as can be.
That being said, maybe you'd like to try the more modern IMAP, Comcast provides it on request:
https://xcsignup.comcast.net/onboardingapps/imapYou will also need to add the account into Aqua again, using IMAP, since the default for @comcast is POP3.
When adding the account, press Manual after entering your email / password and change IMAP to POP3 near the top.