Managed to get the result I wanted after fumbling around a few steps in-between.
Weird things start happening if you forget to save and commit your files on a branch, and then try to move to another. What I had happening was the master branch copied over the scene from the path I was going to merge (but hadn’t yet) and the path to merge had a duplicate of that same scene copied to it (probably because I didn’t ahve a scene with the same name).
Fortunately I was able to discard changes on the master and then save and commit the merging branch and everything went smoothly from there.
Lesson learned: always check your saves before touching source control. (Apparently just hearing it wasn’t enough for me 
)