I think if they do have any issues, they will be directed at the school. If you didn't have the clearance, they shouldn't have trained you. The chances of any repercussions against you I would say are extremely remote.
In defence of the flight schools, it's a silly system that they have to contend with. Fingerprinting can be done on arrival if the original paperwork is completed earlier but even then it used to take 1 week to process them. I'm not sure what the current regs are though.