For some reason when you clone a workflow and it has branches you cannot change the property the brnach is based off of. You have to delete the branch completely and rebuild the branches. The work around is create the new branch above, but then you have to choose 1 branch to keep and the others are deleted, as long as you only have 1 branch with items it is ok, otherwise you have to recreate other branches. The branch property field should be editable.