I had this problem too. It's annoying but doesn't seem harmful to leave it the way it is.
The only fix I had was to delete the email account and then re-create it.
Yeah it's just an annoyance really. It now says "-2/0", while my empty deleted items folder has a 2 next to it. Weird. I noticed an e-mail dated Dec 31,1969 just before it went to -2. I always delete everything anyway since all messages are saved at home, so I suppose I could delete the account and set it up again.