Nope, no 0 byte items are showing up. Remember, these four titles refuse to show up on my home screen as well.
Really am stumped over here.
Can you see the original items in sysNAND data management? If you can, remove them from sysNAND and they will likely work in emuNAND properly. Either that or you can just start completely fresh and wipe everything, relink your NNID and redownload everything from eShop. If it was the anniversary Four Swords though, I'm not sure if that really links to your NNID since it was a limited time download.
Edit: The big thing here is make sure you back up. as long as you have a backup before doing anything you are fine and can do basically whatever you want (short of something you know will brick the device). I recommend backing up and doing a few different things.