Except for user #1, which is pretty much reserved, it would not be an extreme difficult job to renumber everyone back to their old member number in threads.
Most time would go in being careful, not the actual doing of it. You would need a little modification in the migration tool to not throw away the temporary tables it uses for the migration. There is table called ubbt_memtemp used to remap users from old to new. You could use that to get the usernumbers back again.
As far as the numbering goes, by default it starts with #2, and just numbers up. So depending on the number of deleted/missing users, the new member# can differ a lot from the original.