I personally make a scene with all my sprites with body/collision child nodes. In that scene (.tscn)is where I can manage my collision boxes, then once I'm done I export to a tileset (.tres). So I do have to re-export and make a new set. So I guess that doesn't help too much, unless you are recreating every sprite/body/collision in a new file each time.
So maybe just keep that scene file to do future editing maybe?