At the point when Lucifer kills Bobby, Crowley owns his soul. So Bobby should have gone to Hell at least briefly. So it seems like one way or the other, Bobby's contract with Crowley should have been complete. When Castiel brought him back, it should've been with a clean slate.
Dean & Sam are hoping that Lucifer is unaware that they have the rings that form the key to his cage but even if he missed that they had taken rings from War, Famine & Pestilence, the fact that Chicago was not destroyed the way he ordered it to be would lead Lucifer to only one conclusion. Death had found a way to disobey him. Which would have lead him to at least suspect Death didn't have his ring anymore.
At the end Castiel says he is returning to Heaven because with Michael in the cage there is chaos up there since no one is left in charge, to which Dean replies "so you're the new sheriff in town eh". However the Archangel Rafael is still alive, so it stands to reason he is in command of Heaven now, which means Castiel would have to fight him for control. Even with the new powers given to him by God, Castiel is no match for an Archangel.