Help! mail dissappears when switching from junk training to automatic mode

I'm a new Mail user recently switched from 20 years of Eudora. I'm using Mail with a standard POP account. I've had no trouble setting up mailboxes and importing my old mail.
I've been using junk filtering in training mode for the past few weeks and want to switch to automatic mode. When I tried doing this, all of my inbox messages suddenly disappeared. I quit mail and rebuilt my inbox and found myself with thousands of duplicated messages. I'm using Andreas Amann's remove duplicates script to clean up my inbox (it's taking forever but working!)
My inbox has about 7000 messages currently. My practice with Eudora has always been to keep the current year in the inbox and archive at the beginning of the new year. I'd like to continue this with Mail.
A couple questions:
1) will rebuilding a mailbox cause duplicates? When should one use rebuild?
2) do I just need to be more patient and let mail do its thing when switching from training mode to automatic?
3) is 7000 messages considered too many for a single mailbox?
Any help much appreciated. Many thanks!
--dhl
Powerbook 15" Aluminum Mac OS X (10.4.8)
Powerbook 15" Aluminum Mac OS X (10.4.5)
Powerbook 15" Aluminum Mac OS X (10.4.5)

1) will rebuilding a mailbox cause duplicates?
No.
When should one use rebuild?
This question doesn’t have a simple answer in the case of Mail 2.x and POP accounts.
2) do I just need to be more patient and let mail do its thing
when switching from training mode to automatic?
I think so.
3) is 7000 messages considered too many for a single mailbox?
There is a limit on the overall size of individual mailboxes rather than on the number of messages stored in them -- see Overstuffed mailbox is unexpectedly empty.

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