Mail deleted a current inbox and restored an old deleted inbox. It won't restore from Time Machine, and I'm missing archived emails from the old account. I'm pretty sure there is other stuff missing, but it's hard to tell. Any ideas why it would do this?

Our Mac was working fine last Monday, then Tuesday morning one of our current inboxes was gone, and an old, archived inbox was restored--twice. Other than some trouble-shooting on Tuesday, we've pretty much left things alone as we were busy doing other stuff.
I tried restoring the files from Time Machine, but it didn't work. I followed plisk restore instructions--nothing. It's a mess. We have no idea what would have caused this. We're above average users--we weren't mucking about with anything. It was just so strange.
I went back into Time Machine, and it just makes no sense that I can't restore anything. We're now missing important emails--nothing too tragic, but still a pain in the butt. Thankfully the current inbox that was somehow deleted had a back-up on our email server, but the archived/deleted inbox file that was magically restored had all the archived emails that we kept deleted.
Any ideas would be wonderful.
Thanks!

Hello,
Could be many things, we should start with this...
"Try Disk Utility
1. Insert the Mac OS X Install disc, then restart the computer while holding the C key.
2. When your computer finishes starting up from the disc, choose Disk Utility from the Installer menu at top of the screen. (In Mac OS X 10.4 or later, you must select your language first.)
*Important: Do not click Continue in the first screen of the Installer. If you do, you must restart from the disc again to access Disk Utility.*
3. Click the First Aid tab.
4. Select your Mac OS X volume.
5. Click Repair Disk, (not Repair Permissions). Disk Utility checks and repairs the disk."
http://docs.info.apple.com/article.html?artnum=106214
Then try a Safe Boot, (holding Shift key down at bootup), run Disk Utility in Applications>Utilities, then highlight your drive, click on Repair Permissions, reboot when it completes.
(Safe boot may stay on the gray radian for a long time, let it go, it's trying to repair the Hard Drive.)
If perchance you can't find your install Disc, at least try it from the Safe Boot part onward.
If 10.7.0 or later...
Bootup holding CMD+r, or the Option/alt key to boot from the Restore partition & use Disk Utility from there to Repair the Disk.

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