Mail Preferences and lost Messages

Had an issue after a software update: finder constantly relaunches. Tried, PRAM zap, reinstall sys, removing com.apple.finder.plist preference. Nothing worked.
Then I relocated my entire preference file. Now the problem is gone, it was some preference, I do not know which one.
Now I have to set up some programs again, or swap in the prefs from the old folder. The problem is that I have no mail boxes on my mac in mail. All of my messages from the years, catagorized into folders, are gone.
Looks like the first time I every opened mail. I have original prefs folder and all its contents, however if I swap the old prefs back into the lib, most prefs return on restart, however there is still nothing in mail and the finder relaunching error resumes.
Where did my mail go? Did new preferences for mail overwrite my entire mail archive? How can I find them? Where did they go?
Unfortunately I have been meaning to back them up ever since I lost the last backup. Too many good numbers in my emails, user names, passwords, activation codes, directions to Eden. I want them back!
Ideas?

No real help from me I'm afraid but just had a call from my brother who was just lost all his mail setting and messages, mail is appears as if it was started for the first time. His Mail folders in the Library have his pop and mac account folders but no contents.
Have you checked if the messages are in your library? (Home > Library > Mail)

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