I'm only guessing here, I don't have any scientific basis for saying this, but:
- milk is stored in a fridge at 4C - I assume this is to help prevent bacterial growth
- chocolate has an incredibly long shelf life (relative to milk) if it remains unmixed with anything
I would have thought it best to (1) keep the milk in the fridge as long as possible for bacterial reasons and (2) not mix the chocolate with anything else, so that if you don't use it all, you can let it set and reuse it later.