When you configure the max runs for an event, the system will not count any runs over the max towards their best time of the day (or season standings).
This applies on a per registrant basis, so a driver with multiple registrations will have the max applied to each registration and not to the driver as a whole.
So what if I decide to increase the max number of runs during an event?
No problem, simply change the max number in Event Setup, then click the Recalculate Event to update any existing runs that may have been excluded.
Max Number of Runs is currently for the entire event.