I am building a route and am having problems with junctions disappearing when I go back to play to session after I save it. This doesn't happen with every junction, just a few.
Self made route by any chance?
What could be the case is that some junctions are not saved to the route layer but for some reason have ended up in the session layer.
I find junctions have disappeared but have determined that in deleting something close to one it is deleted accidentley.
Generally this happens when tidying up trackwork and adding/removing trackside objects such as signals.
One generally find's out they are missing when trying to run a consist on a route.