Mail - 178 Mb of mail on HDD, not in Mail app.

Hello!
I have 4 accounts - a .Mac, a Gmail, a Yahoo, and my school's POP account. In all 4 acounts combined, I have about 240 messages in the Mail app, or about 60-70 MB - I trashed the rest, as they were either junk, or I didn't need them any longer.
However, the Yahoo folder in my ~/Library/Mail/POP-(email account) is 178 MB - 100 meg (324 messages) is the inbox folder, while 78 meg (247 messages) is in the sent folder. My question is, where did they come from? Why are they here?
I deleted most of these, then right-clicked on the trash folder and selected "Erase deleted messages" - so I'm clueless why they still exist. I beleve some of them may be current, as the date modified (for the yahoo) folder is today. However, no folder inside has been modified since august...
So, my questions are:
1. Why should they still be on the hard drive?
2. How do I get rid of (trash) them, without deleting anything I need (that is, anything in Mail)
3. How do I tell what is new, despite FInder saying that nothing has been modified since august?
Thanks,
-Dan
PS: Upon closer inspection, I have 2 yahoo folders- one has "@pop.swbell.yahoo.com" after "@swbell.net" - which is the proper ending for the email, although a 3 MB yahoo with only "@pop.swbell.yahoo.com" is modified today (now) - seems correct. Odd, perhaps I changed some odd setting...? The big yahoo folder still says modified-today, although I may have moved something accidentially.
15" 1.67 Powerbook G4 (Jan 2005), 400 mhz AGP Sawtooth G4   Mac OS X (10.4.8)   4G Clickwheel and 5G Vid iPods

If you are accessing a single Yahoo email account with the Mail.app which is provided by your ISP (swbell), you should not have two Yahoo POP account named folders within the Mail folder at Home > Library > Mail.
Did you make changes to your existing Yahoo account in the past and/or try creating the account again in Mail without deleting the existing account first?
With the Mail.app quit and using the Finder, move the incorrect account named folder from within the Mail folder to the Desktop.
Launch Mail and if everything is working properly and the Yahoo account's Inbox mailbox and Sent mailbox contain the messages that you haven't deleted and need to keep, check within the Mail folder to confirm there is a single Yahoo account named folder and another Yahoo account named folder was not re-created.
If so, you can delete the 2nd/larger Yahoo account named folder moved to the Desktop.

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