Compaction Error in Mail etc.

Yesterday I started getting a compaction error from Mail when I tried to delete large portions of the Inbox. Although I could delete a few emails at a time and then quit. they were back after the next compaction. Today I tried to troubleshoot it, and I think I made it worse. Note: I was unaware of the "Rebuild" mailbox option.
I eventually found this forum discussion and it sounded like my problem, so I tried it:
With the Mail.app quit and using the Finder, go to Home > Library > Mail > this POP account named folder (named by the user name and incoming mail server for the account).
Move the account named folder to the Desktop. The account named folder contains all mailboxes associated with the account such as the account's Inbox and Sent mailbox.
Launch Mail and a new account named folder will be created automatically by Mail within the Mail folder.
I tried Mail again, and now I somehow had lots of junk mail back which I'd long since deleted, in my old Inbox. I was also missing some emails, from Jan. 2, 2007 'til now. I "got new mail", and it's only from Feb. 5 2007 'til now (1 month on the server.)
The size of the old Inbox was 96.4 MB. After importing it, it's 87.2 MB. Would that account for the missing emails? If so, how do I get them back?
iBook G4   Mac OS X (10.3.9)   22 GB free on hard drive

Thanks for the response. Sorry that was so confusing.
I found the "instructions to import the old mailboxes from the original POP account named folder moved to the Desktop" in another thread, and I'll be darned if I can find that thread again today.
(This should be a bit more clear.)
I removed the PoP account to the Desktop, opened mail so it recreated the Inbox, and imported the contents of the original PoP folder into mail.
After importing, I had the imported Old Inbox containing deleted junk mail which somehow returned, and some emails were missing. I tried the same deletion of large blocks of mail that caused the error message in the original Inbox, only now it worked perfectly.
> I "got new mail", and it's only from Feb. 5
2007 'til now (1 month on the server.)
This is for/within the old Inbox mailbox that was
imported from the old account named folder moved to
the Desktop?
Nope, the new mail was in the original Inbox-mailbox, which was clear until I hit Shift-Command-N. The Old Inbox is in its own, newly-created-when-imported mailbox.
Pre-import Old Inbox contents:
content_index 3.7 MB
content_index-(null)-303 2.4 MB
content_index-localhost-257 2.6 MB
content_index-localhost-393 948 KB
Info.plist 4 KB
mbox 86.4 MB
tableofcontents 232 KB
iBook   Mac OS X (10.3.9)  

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