Seems like most people that report this issue are using an IMAP/POP email account.

This is in an office setting using an Office 365/Exchange mailbox.  It's happened four times in the last month.

I have the user's mailbox configured in Outlook 2011 on his work iMac, home iMac, Macbook plus his iPhone and iPad.  It's also configured on his assistant's iMac.  Six total devices.  All Office updates have been installed for OS X on the four Macs.

The dozen subfolders in the user's Inbox disappear without a trace.  They aren't in the "On My Computer" section, they aren't in Deleted Items, they aren't moved to another mailbox in Outlook, they're not in OWA so the deletion is syncing back to MS' servers.  They're simply gone.  This isn't user-error, you can't select-all and just delete a dozen folders accidentally several times in one month.  You can't delete folders from an iOS device.

After the disappearance Outlook still functions properly and syncs back to the server.  After the folders are gone I can create a new subfolder that shows up in OWA.  If I move items to the new subfolder that change is reflected in OWA as well.

The current work-around is ridiculous, the user powers off his Macbook every morning and disconnects it from his home wireless network.  That way if the deletion bug strikes he can go home, leave his Macbook offline, export the subfolders, connect his Mac back to the Internet, let Outlook sync all the deletions and then import the recently exported subfolders.  That is absurd and he's lost patience.

I've tried rebuilding the identity on his main computer (the office iMac) and the folders do not return.  

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If I search for an email that was stored in a subfolder in Finder/Spotlight it DOES turn up but we cannot open it.  It says "this item cannot be opened because it's not associated with the default identity".

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Are there any data size limitations that I need to be aware of on the local computers?  Although I'd imagine that'd cause the user to simply stop receiving new messages, not make several folders vanish into thin air.

The only options I see at this point are:

1) Export the folders, delete all old identities on the four Macs and create a new identity on each, then import the folders.  That seems crazy and not something I'm willing to do on a recurring basis if this keeps up but I'll try it once.

2) Transition to Apple Mail.

Any ideas?  Thanks!