I'm not sure if this is entirely Dawnguard related but for a large portion of the game on one of my characters ever since they completed the Dark Brotherhood I have been using "Abandoned Shack" as my home (for about 70 hours). I was given the key so I assumed it would be treated like a home and so I stored a lot of things in the chests there. Somewhere in between "Unseen Visions" and "Touching the Sky" all the items in one of the chests has disappeared apart from about 5 that seem to be related to quests. I had a lot of things in there I didn't want to carry but I wanted to keep, dragons bones/scales, daedra hearts, black soul gems and quite a lot of unique items I had collected along the game.

I've found a save at the end of "Unseen Visions" where everything is still there and so I am faced with moving everything to a bought house and doing "Touching the Sky" all over again (which was quite a big quest) or just leaving it and moving on.

What do you think could have caused this? Was it because it wasn't a proper house? Did I maybe have too many items in one chest? And could it be related to the Dawnguard DLC or could it have happened at any point in the game?

You have too many items in there it just takes longer to put things in and take them out, they do not ever vanish. I think it was just the container you had them in respawned, it is not a good idea to use non player owned storage for any length of time.

^this^

Alright thanks guys, I've gone back to the old save and bought the house in Markarth, i should have done it ages ago really.