Actually the best way is better planning at start, having your story finished at least roughly and knowing what you need at start and implement all those variables in first update already. Then again these devs are pretty inexperienced most of the time, so it is understandable they make mistakes like that. At a certain moment though especially when game gets bigger it gets time to remedy those early mistakes.
True, a decent amount of devs are not super experienced & realistically speaking we should not assume they are just b/c they are making a game.
And no matter how skilled or knowledgeable a dev or team may be, no one can predict how or when a newer version of Renpy or whatever will affect the games pre-existing codes or whatever.
My only recommendation to any & all devs is = just make a scene gallery & if game has multiple paths then when a new version releases give player option to start from new version & choose what path your playing.
Doing this seems better that spending god knows how long finding what changed & how code was affected by new platform version