Ok thought you meant something else, when you said patching.
All the informations can be saved, so cant see why you shouldn't be able to reload it, if you update the game, unless you do something that would require something from the save game that is simply not there. I haven't worked a lot with the build in save functionality, but if you are careful and plan the game well, then why not
However the persistent layout I don't think will help you a lot, as it will make things persist as you switch layouts, but if your save games are screwed then it wont work anyway. What you want is to load an old save game for an updated version of your game, so I would check that out first if I were you, if I understood you correct that is