Clock didn't start on a last Second Shot

[splitveer]

NFHS Rules:
A1 has a throw in with 4.6 seconds left. Team A is down by 1. We have talked numerous times with the clock operator about starting the clock on the chop. The ball is thrown in bounds and legally touched. The clock starts at least a second or two late. How should we handle this situation?

Let it play out and manually count?

Kill the play once we know the clock hasn't started and restart the situation?

Thoughts?

Does it change when there is only 1.2 seconds on the clock?

Thanks