I believe it's mostly to do with difference between the xml data stored in the ved/vis files & that stored in a save file. If you say update some graphics, then it's probably not an issue, same with most action parts. The problem is most likely to do with new/updated/removed conditions, values & all the other things that get stored inside of a save file.
If you create some new conditions the data for those won't be in the save file & the game will have to base it on the ved/vis data. Same thing if you edit or delete something as the engine will be trying to locate something that may no longer exist.
I'm not 100% sure on exactly what gets written to save files, but I surmise it's mostly stuff, like conditions, values, positions of animations/objects/characters & so on.
I recommend trying to iron out your game as much as possible before you release it. As a quick fix you could always personally generate & share some save files yourself from various parts of the game. Maybe the beginning of each chapter - bit shit, but it's better than nothing.