Wait, you're saying that some of your town square saves didn't work?
Ah, I guess I'm just surprised you don't make a habit of saving in the town square after every significant event/dungeon, what with the sheer amount of updates this game gets on a regular basis. You'd have lost your save long before ever making it to the Will/Power Temple if you forgot to save in town square THAT often.
Still, try to back up your saves before you uninstall the game so that when you reinstall the version they belong to, you have something to get back to town square with rather than starting over. Trust me, you don't want to be caught out every time you update your game.