Losing all of the saved data from the previous version is painful.
Please consider looking carefully at building save-game versioning and compatibility. There are standard solutions for this. Typically, you’d store a version number in the saved game, and when loading, migrate the save data forward using migrations defined for each version. Anything that isn’t stored at all starts out initialized to the default (e.g. new upgrades start out unpurchased), while anything that has changed gets migrated to account for that.