"On my Mac" folder including all my subfolders in Mail have disappeared after Yosemite install! HELP!

"On my Mac" folder including all my subfolders in Mail have disappeared after OS X Yosemite version 10.10.2 install! What should I do?

Quit Mail. Force quit if necessary.
Back up all data before proceeding.
Triple-click anywhere in the line below on this page to select it:
~/Library/Mail/V2/MailData
Copy the selected text to the Clipboard by pressing the key combination command-C. In the Finder, select
          Go ▹ Go to Folder
from the menu bar. Paste into the box that opens by pressing command-V, then press return.
A folder window will open. Inside it there should be files with names as follows:
          Envelope Index
          ExternalUpdates.storedata
Move those files to the Desktop, leaving the window open. Other files in the folder may have longer names that begin as above. Move those files, if any, to the Trash.
Relaunch Mail. It should prompt you to re-import your messages. You may get a warning that the index is damaged and that Mail has to quit. Click OK. Typically, the process takes a few minutes, but it may take hours if you have gigantic mailboxes. In that case, you may be able to speed things up by temporarily adding your home folder to the Privacy list in the Spotlight preference pane. Remove it when Mail has finished importing.
Test. If Mail now works as expected, you can delete the files you moved to the Desktop. Otherwise, post your results.

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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.
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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.
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Hi Eric. Thanks for your response.
1. All the non-archived sub-folders already appeared under “On My Mac,” so they weren't hidden.
2. A restart helped, in fact. I first made a copy of the entire Library>Mail folder so I would still have all the .mbox content. Upon restart, Mail automatically created its own Archive. Fortunately, it contained all the subfolders in the manually created Archive mailbox that had disappeared. Apple apparently reserves the term "Archive" for its own use in Mail. I found another thread that arrives at the same conclusion and suggests a fix for a related problem: Re: Deleted my 'On my Mac' folder in Archived mail after Mountain Lion OS X update - all mail lost - how to retrieve?
3. I believe the answer to #3 is yes; she'll need to drag her non-archived subfolders to Apple's newly created Archive from now on.
4. I copied them along with the Library>Mail folder, so I'll have them if I need them.
Thanks again for your suggestions.

"On my Mac" folder including all my subfolders in Mail have disappeared after Yosemite install! HELP!

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