No, I meant bottom bracket. The point I was trying to make (which must have been unclear) is that if a bottom bracket, which supports the weight of the entire rider pushing down on the pedals can be ok with less than the maximum amount of ball bearings, than surely a headset will also be ok with a few missing.

I wouldn't worry about trying to put the 3 loose balls back in. Just coat everything with grease when you install your new headset. That way the bearings will stay in place during assembly.