Which d-orbitals split according to CFT?
The $d$ orbitals that split are the $(n-1)$ $d$-orbitals because they are the relevant ones that do chemistry (because they have the electrons).

If the orbitals are degenerate, it doesn't matter whether they're filled or not, the energy level is the same for all the degenerate states. So it also doesn't matter if they're filled or not, the energy states will split up according to CFT. 

The compound only "feels" this raising or lowering of energy depending on how many electrons are filled in into the different orbitals after splitting.

To maybe clarify some confusion: The existence of an orbital doesn't mean that the electron has to be in there, it is only a mathematical construct.