After crash, how do stop apple mail (os 10.7.5, applemail 5.3) from pulling in old mail on reboot

I've got a frustrating problem and need your help.
My Mac pro (os 10.7.5) froze so I was forced to push the button to restart.
After reboot, apple mail 5.3 auto opened and pulled in thousands of old mail that were long ago deleted.
Now, is there a way to mass delete the new/old mail that reappeared without losing what mail I wanted to save?
More importantly, how can I avoid this the next time my mac freezes because it's not the first time it's happened and it's does not happen on every crash.
Please advise
Thanks

The mail that keeps coming back is what is still sitting on your mail server. If this is a POP mail account you can configure Mail to delete mail that has been downloaded.
Click Mail in the menu bar and select Preferences. In Preferences, click Accounts and select your mail account on the left, then click Advanced. There you can decide on the setting you want: "Remove copy from server after retrieving a message", to for example After one day.
If you have an IMAP account  - say gmail - the process is different. Post back if that is what you have.

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