Thanks for the quick reply! I assumed that was the case.
Here is a simple example of what my data will look like: JSFiddle
To keep this simple, a user can be working on adding questions(Q) and Answers(A) to this tree. They will beable to move around, relink, add more questions/answers, etc.
So maybe they only want to view a certain path of which they are working on to keep the view from being massive and just continue to add questions/answers from the opened nodes. Sometimes a user will not finish everything at once, so I am saving the positions of each node in a DB so they can resume it later on (Positions will be unique by user). The problem is that the hidden nodes does not have x/y coordinates. So when reopening the nodes, the nodes with "null" positions stack on top of each other (Which could be hundreds of nodes).