Maybe there's more than one Skaro?The thing is Skaro was destroyed in the 7th Doctor's era, and yet came back just before the 8th Doctor came about, and then was destroyed again in the Time War, but then, there it is.

The one in the TV movie onward* could be a conquered planet they turned into a new home world and renamed Skaro.
*Don't remember if they said it was destroyed during the Time War