The problem is though, Skaro was most definitely destroyed in Remembrance of the Daleks, when the planets' sun went supernova thanks to the Hand of Omega (In screencaps from the game, it appears Skaro still has a sun). This was well before the era of the Time War. Skaro is also depicted as still being around in the 1996 TV Movie. Is there any way this can be explained?
The Daleks tricked the Doctor into believing he had destroyed Skaro, but it was in fact another planet, beginning with A. It was mentioned in a novel I think.
Granted, canon doesn't usually flow between mediums but I tend to believe this is the best solution.
EDIT: The planet 'Antalin'.
http://en.wikipedia.org/wiki/Skaro