Issues are usually caused by missing xml data. If you add, remove or change conditions, values, the name of something, etc, then it's possible that it could cause various issues. When data is missing I believe it defaults to the xml data stored inside of the ved / vis file instead - I'm not 100% sure.
One of the best things you can do when exporting your game is to make sure you export everything individually as opposed to including everything in the main data.vis file (or whatever you happen to call it). This makes it easier to release various updates. You could also I suppose manually generate the save file yourself & include it in the update with a file path that automatically places it into the relevant localAppDir folder. Don't ask me how as I'm not sure off the top of my head, but it should be possible.
As for the in-game saves & autosaves / quicksaves... I have no clue. My suggestion would be to get the game as bug free as you possibly can before officially releasing it.