You had the server shut down when you did the over-write, right?
And, how old was your old ULX?
It's likely you have a corrupt original ban.txt. Old versions of ULX sometimes allowed players with assorted ascii that lua didn't like to read to be stored in the ban.txt, which would corrupt it.
If you had permanent bans in it, your server's "Real" banned_user.cfg list should already have all your bans.
Our ban.txt is really only needed to store the who banned, the reason, and when temporary ban, the length of time across server sessions.
(For whatever reason, Steam doesn't keep temp bans across server sessions)