I realize there is no file format involved IN THIS CHANGE. What I was implying there was a possible file format change to better support this specific use case, and I concluded that it was hard or impossible if it meant a file format change (i.e. to support net lists independent of the wiring lists -- as it appears now that the net list is DERIVED from the wire list, which in my opinion wiring connections is merely a display issue, the net connections should be independent of that, and I don't think it is )
Yes, the other cases you mentioned would be difficult, I know. Power pins suddenly becoming un-hidden, or pins moving about in a box...
That's why I said it would probably require a file format change, to separate the net list from the wire list. And I did say "best effort" to reconnect them. Things like boxes growing or shrinking are equally trivial. Pins and wires moving about can be handled by the same display algorithms that move connections above, below and around things when you move a wire interactively. It's all possible, but I concluded that to support it might require a file format change that is likely not going to be done, simply because this use-case is not going to affect many people. For myself it was a one-time thing, and I'm past it now. And definitely using you're own vetted libraries will further shield people from this too.
So my conclusion is that it's not worth it, and I'm happy with that. As I said, there are other areas in Kicad that need work, and that are worth more to more people than this one time event.