this is strange.
I am not doubting what you are saying Josh But, I have used threads for a long time (since 1999 I think) and I have over that time actually dleted many groups. the Key I always made sure that the group was empty before I deleted them and no forums used the group. I can imagine myriad problems if you had users in groups that had been deleted but I do not see where other problems could arise? What sort of problems could you have? In this entire time I have not had database corruption or other database related problems.
