bought some scrap batteries yesterday

I can't stand a thief, they will take whatever they can get away with and whenever. With the scenario you describe, the "boss" is dealing with two new people. A new employee and a new buyer, the only thing he knows for sure, he has a problem he may not have anticipated and he will need some time to help him decide on what (or who) works for him with honesty and integrity.

You did the right thing by letting him know your not OK with him refunding your two "missing" batteries. Speaks to your integrity and with time he will know, you are someone he can trust. The "new" employee will be tested, you can count on that. Let it go for now, you need to choose "battles" that have positive outcomes for yourself!