Got the same issue and, after the initial panic, also found the post deepc is suggesting. That post from miky_jr should be stickied - it's a life saver!
Luckily I did not have to recover a huge number of mail accounts. But, how does one avoid this happening again?
What is causing it? The Zarafa module upgrade or the Users and Computers module upgrade?
miky_jr wrote in his post from March 2013:
After knowing this annoying side effect we will change some zentyal implementation to fix this behaviour (sooner than later ).
Seems this has not been done yet...
I see there is now another upgrade of the Users and Computers module and I am weary of installing it. Would hate having to re-link all those orphaned Zarafa stores again and having to deal with the mail which arrives in the meantime in the new, empty stores.
Any suggestions for a Zentyal / Zarafa beginner?