Cannot find or move mac mail data

Question

I recently reformatted the hard drive of an intel macbook pro, installed 10.5.7, and used migration assistant to restore user files. After starting Mail, it asked to import messages, which it did fine. However, upon inspecting ~/Library/Mail, there is no longer a folder for the POP account in question, only a file entitled "envelope Index", which is small compared to the size of the original mailbox (~ 1 GB). Although all the main was present and could be read (including attachments), the mail did not appear to exist anywhere on the computer.
Confused, I deleted the entire ~Library/Mail folder, and disconnected the machine from the external drive containing my mail archives. I then restarted Mail, assuming there would be no messages. However, after restarting, it asked to import mail, I said OK, and it re-imported the messages, apparently from nowhere. The machine was disconnected from the external hard drive, and the mail folder had been deleted, yet there the messages were, intact and readable.
Apparently Mac Mail is using some kind of hidden files to store mail, which is very disconcerting because it now means one cannot trust the finder to move and backup mail files. I'd appreciate it if someone could educate me on where Mac mail is actually storing the mail, since it is apparently no longer in the ~Library/Mail/POP-<account> folder...

Answer 1

Finally figured this out, and the answer is a bit scary...
This mail account was originally established under OS 10.3 (Panther). In those days you could specify the Mail home directory in the Advanced tab of Mail preferences. In this case the HDD had 3 partitions, including a dedicated volume entitled "Mail". The mail was kept in Volumes/Mail/MailFolder.
When the new mac was established under 10.5, Migration Assistant copied the com.apple.mail.plist file to the new drive. When a new account was defined with the same name as the old one, the mail was imported to a unix directory Volumes/Mail/Mailfolder, even though this directory did not appear in the finder. The mail did not seem to exist anywhere because the directory did not appear in the finder, and the Mail prefs did not allow you to see where the directory was. What is especially odd is that if the directory was deleted, it would regenerate every time the mail was reimported.
Solution was to delete the plist and start the import over again. In this case the mail was imported properly to Library/Mail.
Rather scary, since it seems Mac Mail was writing to a partition that does not appear, even in Disk Utility. Does that mean it was overwriting space of another partition? If so, it seems to be a major hole in the OS.