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?

When you deactivated the DLC you removed all the DLC content (Items, NPCs, locations, quests etc) from the game. In fact, you would have got a message about missing content when you loaded the save game in Tranquility Lane.

When you subsequently resaved, you presumably just saved over the file you previously loaded? As far as the game is concerned now, the DLC were never installed.

You then activated the DLC and it was as if you were doing so for the first time. If you want anything back you'll have to either load the earlier save game or redo the DLC quests.