I've got a user who's post office and client was recently upgraded from 2012 SP4 to 2014.2.2.

This user is now missing thousands of emails and hundreds of calendar appointments.
In addition, hundreds of his folders are missing too, (and this is the strange bit) when viewed in the morning.
Basically, any folder after the letter 'Q' is not shown (including his system Trash folder).
In the afternoon, however, all of his folders are visible (although the missing emails and calendar appointments are still gone).

If he creates a new folder, suddenly all of his other folders appear. However, if he then closes the client and reopens it, the folders after the letter 'Q' are missing.

If he accesses his mail via webmail, all his folders are there (always).

I've tried numerous Mailbox/Library maintenance tasks, including Structural Rebuild, Recreate User Database, fix system folders (via resfldr) and nothing has made any difference.
The folders also haven't been moved anywhere weird - they are exactly where I expect them to be, when viewing his mailbox in webaccess (or in the afternoon, on his client).

Does anyone have any suggestions?