Hey I was making the genius challah recipe. first proof left on kitchen counter instead of fridge Should I shorten second proof

No. you need two full proofing, wherever they take place. It's not the total time, but the required change in size or texture of dough.
First proof in fridge, as all fridge proofing, slows down the process and improves the flavor.
When you did that proof on counter, at room temp, you reverted to frequent or regular home practice. No harm.