Clara prevented the events of The Name of the Doctor in The Time of the Doctor by getting the Time Lords to give the Doctor another regeneration. So this means that The Name of the Doctor could never have happened, right? Well I don't know about that, it was supposed to prevent it. But in S8E2 the Daleks don't remember the Doctor, because Clara/Impossible Girl wiped their memories. How is this possible since The Name of the Doctor events never technically happened??
Two possibilities present themselves.
First, we have no idea if the events that created the setting for The Name of the Doctor will still happen or not. Just because they didn't happen during the Siege of Trenzalore as depicted in The Time of the Doctor doesn't mean there won't eventually be another battle there that will result in the Doctor's death. That was an awfully large graveyard that we saw there, which doesn't really seem to match up with the state of things by the time the Doctor regenerated.
Second, the only thing we know for certain from Name is that the Doctor is buried on Trenzalore. We are given the impression that there was a battle that the Doctor led and died at the head of, but that's all an assumption that we have no proof of. Maybe the Church of the Papal Mainframe consecrated Trenzalore after the Siege and now the whole planet is a cemetery -- we don't know. The Doctor could simply have programmed the TARDIS to always return his remains there after his death upon learning that it is where he must be buried. His actual death, though, could be from anything and still be centuries or millennia in his future.
In either case, there is no reason to think that Clara's actions in Time necessarily cancel out the events of Name.
if you look at it in terms of when the doctor and Clara episode journey to the centre of the TARDIS, we saw when it happened all the times people died and what they did to rectify it, I have in my mind then when we are watching doctor who each episode we are watching HIS personal timeline, so by the end of the episode we see them go back in time and re-write that day.
so the way I see it is that the name of the doctor was before the 50th in terms of the doctors own personal history then some time later he gets the chance to go back to the time war and fix it, the other doctors are just there for the ride and thats why only Smith and Capaldi remember and because clara is there an follows him along most of his personal history what she has done stays