Surely it shouldn't get in a way of your development plans, so I suggest to just add a simple precaution, like adding a version number to a save file, and refusing to load saves from different versions. Users who still cherish these saves could just get a compatible game version and use it.
@AMDmi3 It's a linear story-driven game, but the current version is disconnected/unfinished. A savegame is not valuable currently.
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