What's a good strategy to overwrite saveGame data during game dev?

Am developing a hybrid game that partially depends on exploration and “lock & key” style progression. As players explore, they discover new things that unlock various aspects of their character. This game is in early access, so currently i’ve basically left everything unlocked to keep gameplay open. I’d like to start issuing builds that implement the lock and key type of system (with things actually locked), but i’m still working with the saveGame data including, removing and optimizing data. I don’t want players to have to redo progression after every build. Is there a saveGame data strategy that will maintain progression, but won’t become corrupt because of new saveGame data object being implemented? I’ve done some beta testing in the past, and noticed that data is reset all the time, but was interested in learning more about this process.