All emails stored "on my mac" are gone?

Upgraded to 10.8.2.  All my Macmail email folders that were stored "on my mac" have been emptied.  I see them in "All Mail."  How do I reorganize/assign them back to original folders?  I've followed other discussions, found them in Library>Mail>V2 and tried to import them from mbox format, but "no valid mbox files found".  Any suggestions?  I have a back up for Time machine, but figure out how to transfer files back to folders.  Thanks.

if you think it's a good idea to store these emails on iCloud - and I would have reservations about it - then the procedure is done in Mail on your Mac.
1. Create a new mailbox, making sure it comes under iCloud. To do this, click the '+' sign at bottom left, and in the pane which opens set the drop-down menu to 'iCloud' and choose a name.
2. Open the mailbox containing the messages you want to transfer
3. Select some messages (don't do a large amount at a time) and drag them to the new mailbox in the sidebar.
Allow time for them to upload before continuing. This will remove them from your Mac. Repeat with other messages and new mailboxes as desired.
Now your important messages are on iCloud, and if it goes down or there is a server error you could lose access to them, which is why I question it being such a good idea. If you leave them on your Mac and ensure you have a backup strategy in place, that might be safer.
However you could do both by following the above procedure but holding the option (alt) key down while dragging. This will copy the messages to iCloud but also leave them in place on your Mac. Obviously you will then see them in both mailboxes in Mail, though only in the one mailbox at icloud.com

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