Yes! This has just happened to me too! If you are a single user I've found that you can delete your email account from your client (in my case OE for Macintosh, but it also works in OE for Win, as I've tried it!) and re-create it as if it were a new account and lo and behold all of your email and folder contents are back again. If you access via web-browser everything is OK.
Unfortunately I've got 80 users on 16 sites across the UK, so there's no chance of me being able to do this on all the client machines. I'm going to have a hell of a lot of unhappy users tomorrow!
As a side issue I didn't notice this on the test server as I restored all of the user data to it and then upgraded to 5.6 and tested it, so it appeared to work fine.
Moral of the story, try the accounts first and then upgrade!
BTW my upgrade was from 5.1.2 to 5.6.
The problem is only in IMAP boxes. Anyone got any ideas?
I'm just off for a deeper search of the archives. IIRC this happened a while back (4.0 to 4.1 I think). Maybe same thing will fix it!
Richard Bruce