I thought that sites without student accounts didn't have to run the UPN reconciliation tool. Is it the only option that you are offered? Can you download a users@site report? My UPN file that I downloaded only contained the accounts that had been designated pupil account status and all of the adult ones weren't listed.
Edu-IT - did you use the admin tools in the old Community Gateway system to create and edit accounts as the WAT tool should perform those functions.