Most the games that use Renpy have only a few variables that are saved and that doesn't change much through out the games development. That's because of the nature of the game type.
They spend most of their time adding story content not adding new features to the game or characters. If they did they would have the exact same issue.
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Like I said this is an issue with the game engine and how it saves. It is just one of the trade offs for making this type of game on this engine.
I tried Renpy myself. If you add a new variable that is saved or remove a variable that is saved it requires a restart.
The exception is if you use a default variable. Using a default variable will reset that value to the default value any time it isn't provided. Default variable will not work well with this sort of game. If lets say you wanted someone's life to restore to 100 when they reloaded a default variable could be a good choice for that if you don't save the life value.
But lets say you add something like a property value which lists the properties the person owns. What default value could you give it? None you come up with would be suitable it would destroy the progress of the game.
The reasons most games don't have this sort of change is they have relatively few variables in comparison and the developer doesn't make many changes of that nature instead they are just adding content. Those are mostly just story based games.
One problem is the progression of his own learning to program which is something a lot of developers are having to content with.
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I doubt most the people new to Renpy fully understand the implication of what all is said in this. Especially when they are new to programming also. I'd bet there are a number of seasoned programmers who don't fully grasp the ins and outs of it also.