Mail in On My Mac disappeared after Mavericks install

Yesterday, after making a complete SuperDuper backup, I installed Mavericks on my lovely bride’s MacBook Pro Retina (Mountain Lion).

Everything went smoothly, and all of her various email archives in On My Mac subfolders appeared and were readable.

She decided to clean up those old email folders. I created a new mailbox named Archive at the top On My Mac level. Throughout the afternoon, she dragged the various On My Mac subfolders with old mail into the new Archive folder. She stepped away for a few hours, returned to continue the archive process - and the new Archive folder had disappeared. The MBP had not been shut down (and still has not).

I checked Library>Mail. Right at the top, there’s a folder marked “Mail Lost + Found” with lots of .mbox content. Just below that is the expected folder marked “V2” with the bulk of the expected mail components. Under its “Mailboxes” folder, the very first .mbox is “Archive.” All the subfolders she had dragged to that folder yesterday do appear in the “Archive” .mbox.

I hope someone will field a few questions, please.

1. Why would the new Archive folder at the top level of On My Mac disappear?

2. What should I do next? I’m concerned that restarting may wipe out the Archive mailbox and its contents, but I’ve read that a restart sometimes corrects Mavericks Mail problems.

3. Assuming I can get her Archive folder visible again, is she likely to run into the same problem if she continues to drag the remaining 10-15 subfolders into the Archive folder?

4. What, if anything, should I do about the .mbox material in the “Mail Lost + Found” folder? At least some of it appears to be duplicates of the subfolders in the Archive folder.

5. Is there a better, more stable archive solution for all this mail? It spans years, multiple IMAP and AOL accounts, and is - or was - neatly organized in subfolders by topic in Mail. Would Mail Steward be able to import this mail, keep the mail organized, and be as searchable as the Mail app? Would it be a good solution to import and reconcile the material in the “Mail Lost + Found” folder? Again, I do have her full Mountain Lion system, including all the Mail, on a bootable SuperDuper drive If that might help create an archive outside of Mail app.

Thanks!