After re-install, strange things are happening with my emails

I had a crash during an optimization adventure with TechTool Pro when I was running 10.4.10. Since I had problems with this version (another issue), I did an archive and install for 10.4.8, with a subsequent upgrade to 10.4.9, and stopped there. So when I moved the mailboxes from the previous system folders to the active ones, my emails "disappeared". The mailbox windows are completely empty. In one mailbox, I "lost" nearly 2000 messages that I needed to archive. On my iMac, I have about 60% of those emails saved and backed up.
I put quotes around "lost" and "disappeared" because I can open the files with TextEdit. They're complete and intact. But I can't open them up within Mail.
I rebuilt the mailboxes, with no success.
So what can I do to get Mail to recognize these invisible email files? Can anyone suggest a way to get Mail to recognize these files?

Rather than tinkering with the contents of ~/Library/Mail/, you should have either restored the whole ~/Library/Mail folder as if it was a monolithic entity, or import the mailboxes by means of File > Import Mailboxes.
That said, if Mail doesn’t recognize the messages in those mailboxes even after rebuilding them, chances are that importing them by normal means wouldn’t have worked either. In that case, you may try using emlx to mbox Converter or Emailchemy to convert the *.emlx files to standard mbox format, then import that in Mail as Other.

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