I can't seem to find anything on why this happens so here I am.

I have BPF that moves through 3 opportunity stages and automates closing the opportunity as "won" upon moving to and creating an Order. This works perfectly when we continue to move through the subsequent 3 order stages. However, when a need arises to go back a stage ( between order and opportunity) and alter something at the opportunity stage, the relationship at BPF is lost. Only a new Order can be created thus orphaning the pre-existing Order and causing great frustration to our sales community.  When looking at the related order subgrid, both the orphan and the newly created orders are there to cause me more confusion. Within the BPF the entities are related. 

Any ideas as to what is going on would be appreciated.