The onus may transfer to the permit authority who could go through the list of results and then bill the race organiser for all athletes who, in their opinion, do not have the correct affiliation.
Races under different authorities will require individuals to declare their affiliation (and quoting their reference number) in order to establish if a levy should be charged.
Some runners will run under assumed names or give fictional information in order to reduce their entry fee. This will create even more difficulties.
The overall effect may be that entry fees for many races will be raised in order to reimburse the authorities and every athlete will suffer.