I think one of the problems I have is in my initial planning and implementation of the scenes
A number of the scenes in my game are re-visited over time after certain parts of the story have taken place, after the character costume has changed, after doors have been opened, places un-covered, lights turned on etc, all of which effect the placement, status and appearance of items in these rooms
I'm doing lots of conditional checking on a few of my rooms for lots of different things, when in retrospect, it would have been more sensible to actually create 3 or 4 separate versions of the same room, rather than a huge "on enter scene" action in the one room.
That way its easier to track a single timeline of when you should enter cave v1, v2,v3 based on a single value or condition.
Hope this retrospective tip, helps someone!