[Viking2054]

Using the tree model, couldn't you put these special sub-plots as a kind of falling leaf from the tree? I mean it could show up either as a sub-plot not attached to the tree at all, but floating off to the right so that you know it is special. Then when you expand that special leaf, it can either have a list of links at the top showing what sub-plots it attaches to, or have arrows that point to the sub-plots or plots they attach to (maybe even a parent plot if that section of the tree is collapsed).

You could also just have a master sub-plot with pointers to it under each sub-plot that could or should have that same information. I'd probably still separate the master note/sub-plot from the tree so you know there is something special about it. I'd also have any attempt to edit the pointer based copy give you the option to edit the master note/sub-plot or force a copy of the master note/sub-plot to be made in the editing location for changes that would become specific to that particular sub-plot.

I hope that made sense.