There is no problem formatting one virtual drive without hurting the other one. That is one reason to partition them that way.
Just be very sure you are pointing at the right address when you format it.
In a single hard drive system that is easy. You just have to be careful if you add a second physical drive. Your addresses will move. There is a trick to prevent that but that would only confuse the issue at this point.
Just be sure you are pointing at D and format it.
