Similar behaviour may appear in some specific situations (like after saving the "master" scene) when using Surface Area(s) and the Forest object in XReffed scene doesn't update surface data automatically - the Auto (Update surface data automatically) isn't enabled. It's generally not recommendable to enable it on large scenes, as it may affect the performance. The distribution preview may in some situations appear wrong, but it should render correctly (and once rebuild, the view-port will be updated too). Please feel free to check attached sample scenes.
In case the problem persist on your side even during the rendering, would you mind to send us such scene(s)? Thanks in advance.