A bit strange if you think about it. If the game offers an VN mode, you should think both modes should be equally upgraded story-wise. Or at least give a clear warning at the start of the game that the VN mode is limited and not advised.
Or - If you don't want to update that mode, than completely remove it. As it is now it can lead to frustrations, or misunderstanding about the upgrades. At least it's not very nice to negelect the users that made the "wrong" choice at the very start of the game.
That does not take away that I think it's a nice game, but it feels unbalanced in that regard.