I was experiencing major freezing in tranquility lane so I turned of all graphics options, all the DLC then quickly did the fail safe to get out of there. I saved after this point. Now I exit, turn the DLC back on and load my save and the DLC quests are coming back as new quests, as if I haven't done them. Is there any way out of this?

My last save is over 10 hours ago! I assume I can't get my items back, but can I not at least get the game to register that I've done the quests? Surely it's still on the save file?

No, you saved after uninstalling the DLC so it's as if you never played them. You can either reload back to before you uninstalled the DLC or you can replay them.

Let this be a lesson: Quicksave is only your friend if you don't overuse it. Always make real save points.