Well, this is officially my first blog post ever. I feel like Captain Picard discovering a new galaxy...
So file merging in Blender isn't everything we want it to be. I went ahead and separated our two main scenes into two separate files, then created a new file with the two scenes merged using File->Append.
Good News: When a scene is deleted, its library goes with it. This means that the merge didn't cause any library/object conflicts (we may see some if the same objects are used in multiple scenes).
Bad News: Actuators that move between scenes break when you separate the scenes. If a given scene doesn't exist, the variable is clobbered in the actor pane (i.e., SCE: Navigation goes blank because it can't see the scene Navigation).
-Fix it every time we merge, or
-instead of deleting the scene we aren't touching, have a total of three copies of the same file. Two are the working copies of the two scenes we will be working on, the third is a manually merged version. To do this merge, we'd create a new blender file and append the two scenes from the other two files. But no, this would still lack the second scene at some point, so that doesn't work. hmmm.....
Thoughts and tutorials on programming