Mail.app downloading old messages again

I have multiple pop accounts. I have it set not to delete from the server for 30 days. In order sync my Macbook and Powerbook, I copied all my mail on my desktop to my Macbook. Everything is there and it works fine but when I check mail it tries to download 3000+ messages.
Basically all the same mail that is there already, from the last 30 days.
Mail.app thinks it has not downloaded it yet. Is there a way to tell it that it has downloaded it ?
Otherwise I am going to make a rule to download all that mail into a new folder then I can just delete it from there afterwards.

Hello, I'd try this...
Safe Boot from the HD, (holding Shift key down at bootup), run Disk Utility in Applications>Utilities, then highlight your drive, click on Repair Permissions...
Open Mail, highlight the problem Mailbox, choose Rebuild from Mail's Mailbox menu.

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    Hello, I'd try this...
    Safe Boot from the HD, (holding Shift key down at bootup), run Disk Utility in Applications>Utilities, then highlight your drive, click on Repair Permissions...
    Open Mail, highlight the problem Mailbox, choose Rebuild from Mail's Mailbox menu.

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