That alter table should actually be

SQL Query
alter table ubbt_USERS AUTO_INCREMENT=3

You will need to use the prune topics to clean out the tables properly, however if it's not working, open up a support ticket with the following info and one of us will manually do it.

In your support ticket you'll need to supply the following info:

Forum URL
Admin Login Info

and the date range that of topics/posts that you want deleted.