Supposedly, New Vegas wasn't retconned after all, the showrunners just accidentally flubbed the timeline. According to Todd Howard, Shady Sands got nuked shortly after the events of that game (which took place in 2281), not in 2277 (the year Fallout 3 happened).

Or maybe you were talking about how Mr. House and Frederick Sinclair, from the main game and Dead Money, respectively, were in on Vault-Tec's plot to nuke the world? IIRC, House doesn't outright say he agrees with the plan, so he might actually have been against it, and this might actually be a canon explanation for how exactly he knew the end was on the way and was able to make his preparations. On the other hand, Sinclair now comes off as a major piece of shit compared to how he was said to be in Dead Money.