I know this because I've dug through the game's save format in a hex editor on multiple occasions and have a basic understanding of how Unreal Engine deals with file handling. I know this because I've written complex file handling from scratch for multiple projects. I know this because this is literally beginner level, programming 101 course material.
This is not coming from a position of ignorance. This is coming from a position as a programmer who has on multiple occasions written complex data storage handling for games and mods. Making a file loader that doesn't crash when a new variable is added to saves is literally the bare minimum in such projects. In the case of the world flags for BotN, like the status of conversations, gates, and keystones, they're stored in the save as a list of strings. We already know the loader supports this because the flags literally don't exist in the save until you open the gate. Allow me to repeat that: the flags don't exist in new saves until after you run through the content anyway.
Invalidating the saves was a deliberate decision to force players to run through the content again.
If you want specific details on what I'm talking about, you can look at the post I made a while back about
using a hex editor to open the gates, before the cheat was well known in this thread.