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As revealed in "The Day of the Doctor", Gallifrey was not actually destroyed; it was placed in a pocket universe. However, nothing suggests this has anything to do with the fate of Skaro.

Although the fate of Gallifrey is known for sure, Skaro is more confusing. Skaro was completely destroyed in "Remembrance of the Daleks", but then it was there during the Time War. They've never explained that. Then it was destroyed again during the Time War and then appeared in City of the Daleks, and again, they've never explained that. So, what does that mean for Gallifrey? Who knows? We don't have enough information to know how Skaro came back either time, so we don't know whether it could apply to Gallifey.

If you turn to the novels, there's a lot more going on.

In War of the Daleks, the Dalek Prime claims that it was actually a fake Skaro that was destroyed in Remembrance, but his story doesn't make sense. The best explanation I've heard from anyone is that when Skaro was destroyed, the Daleks just built a new Skaro and pretended it was the original. So, presumably, after Skaro was destroyed in the Time War, they started building another one, that one was ruined but not completely wiped out, and that's the one the Daleks went back to in City. On the other hand, if you insist that Prime was right, maybe they just used another fake Skaro during the War. Or, putting the two together, maybe they made a bunch of decoys, one of them survived, and they decided that was now Skaro. It may be significant that the word "Skaro" in the old Kaled/Thal language just means "Home".