Okay if anyone come across this because they are having similar issues; in my case it was because I was creating objects on initialising of the game and storing them in an Array. When I swapped levels the garbage collector was deleting the actors I “spawned” as part of the code and was thus emptying my array when the next level loaded.
I knew objects within the level were destroyed when the level changed, but I thought because the data was stored in the instance the data would remain there. Unfortunately that is not the case, when they are deleted they are deleted from everywhere.