I'm not sure exactly what caused the problem, but when I edited the design again from the original page template it worked...
So I overwrote his edited themes with the original again and they seem to be functioning properly. It would be interesting to find out steps to reproduce what causes this problem in the first place, since the only solution I could find was to start over with the original theme, but some steps must bring it to that point in the first place, but I couldn't reproduce it.
Luckily this user didn't have many other updates so starting over fresh won't be a big deal I'm sure, but after it has been live for a while if someone runs into this and has more time invested in making edits it could be a bigger issue.
You can let them know that it appears to be working now and if it happens again to him or anyone else we should try to find out what they were doing recently that may have caused the problem in the first place.