Deleted emails still on my server - where do they go?

Sorry if this is an old topic; I read a buttload of threads about deleting and still have barely scratched the surface but am too impatient to read any more, and still haven't found my exact issue.
When I manually delete an email (which moves it to my trash) and then I either manually delete it from the trash or select "Erase Deleted Messages" from the Mailbox menu, the email appears to be totally gone from Mail but it is still on my ISP's mail server. I know this because my account is merged with a web-based email account from the same company, and they tell me they use the same server and mailbox for both accounts. When I do the deletes described above in Mail and then log onto the web-based account that uses the same server, the email is still there. So how can the email be totally deleted from Mail and yet still be on the server? Is it hiding in the Library somewhere? Will it eventually be removed from the server at the time specified in my prefs' "mailbox behaviors" under "erase deleted messages when"? If I didn't happen to have this back door for noticing that emails are still on the server, how would I know if deleted messages were really removed from the server? And if it is eventually removed from the server, will it still be hiding somewhere on my hard disk?
In case it matters: I have not created any mailboxes of my own in Mail. As far as I can tell I do have anything going on "on my mac", if I understand that term correctly as it is used in Mail.
BTW if I delete emails automatically by checking the advanced prefs checkbox for "remove copy from server after receiving a message", that does remove them from the server, unlike the manual delete procedures I described above.
PowerBook G4   Mac OS X (10.4.6)   Mail 2.0,7
PowerBook G4   Mac OS X (10.4.6)  

I see the "Remove now" button next to that checkbox--exactly
what messages does that button remove? The current message?
All messages? Just the ones that don't have a blue dot next to them?
The Remove Now button removes ALL messages available at the incoming mail server for the account.
To remove an individual message from the server, select the button at the bottom of the mailboxes drawer which has a gear icon.
At the bottom of the menu window that appear, select Get Info.
Select the POP via the Account selection - the account will be already selected if you are accessing a single account with the Mail.app.
Under the Messages On Server tab at Show Messages, All messages on POP server should be selected.
The window below will reveal all messages currently available on the server. You can select an individual message or multiple messages and then the Remove From Server button.

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