User blog comment:Phoenix96/Timeline trouble?/@comment-5767263-20140525042244

It would only be a problem if that were the only way in which time travel worked in the show. There are actually two ways that it can go: Either time stays consistent in a loop (for instance, Dean being sent back by Castiel and accidentally leading Azazel to Mary in the process so that Azazel will eventually kill his mother, causing him to eventually become a hunter who gets sent back by Castiel, and so on), or a new timeline is created (for instance, Balthazar goes back in time and unsinks the Titanic so that all of the passengers survive).

What happened in "King Of The Damned" was the latter, as explicitly noted by Sam at the end of the episode when he tells Crowley that altering any detail can create a ripple effect. However, Crowley was right in saying that Gavin was so inconsequential that his survival had almost no impact on history. Although they are now in a new timeline, Gavin's survival didn't change all that much because he wasn't really important in the grand scheme of things.

As for the whole "Crowley's bones" incident, that now only happened in the previous timeline (just like when Balthazar unsank the Titanic - it had to have sank in one timeline in order for it to be unsunk by Mr. I.P. Freely). In the new timeline, Bobby would have had to have figured out some other way to get his soul back, but Bobby is smart. I imagine he could think of something. Or, maybe he didn't, and in this timeline, Crowley didn't even have to bother with hiring Ajay to smuggle Bobby's soul into Hell. It would have just come there naturally as a part of the deal (but either way, his soul would have definitely been there for Sam to rescue during the second trial).