As someone who has spent a fair amount of time working within other people's code in RenPy, let's just say that I respectfully disagree r.e. the time that would be required to incorporate a simple check/update for the variables that are missing. Even setting up the 'flashbacks' wouldn't be that hard if you wanted to do that. If we are talking dozens of scenes, maybe, but if we are talking just a few scenes, yeah not that hard.
At the very least, I'd suggest an option to 'jump' to the first point of significant divergence from the old story in the dialogue.
When I say significant, if it's something meaningless like say 'well we used to have 2-3 choices, but really there is only one now' simply include that in the 'So you are jumping to here, but before then we removed these other choices, 'cuz they are no longer part of the story'. Most seasoned players that have already played through a few times will know these, and won't be 'thrown off' by the reference. And you can also include a 'I need to go back to that scene so I understand' option for those that need to start from that point.
Obviously, the 'game ending' choices aren't going to be relevant in this case, otherwise you wouldn't advance in the story, so you can simply 'incorporate' the correct choices within the 'jump forward to where the story has changed option'.
Keep in mind the amount of content already ingame, and while yes people could just 'ctrl' through the old dialogue, it's still going to take some time.