Why does it matter whether he uses the stolen money or his own?
Because the entire question is:
How much money did the shopkeeper lose?

, we are not looking at how much the thief gained.
Okay... let's say the shopkeeper used his OWN $100 from the register to purchase his OWN goods, worth $60. Just picked it out of the register and put it back down again. Then? He'd be out $60 in goods that he took off the shelf and took home. If he gave himself $40 change and pocketed that as well he'd be out $100.
Someone's finally thinking outside the box here
But yet again breh, we have to take into account that the shopkeeper is already at -$60 (approx subtract profit margin at which he sells goods) because he purchased his goods from a supplier. So him taking $60 out of his own pocket is him paying $120 (approx) as he's paying for his goods twice.
This is why you don't get high on your own supply, you're paying double.
The change is irrelevant.