Generally, what happens is I use Agent to make a change that has nothing to do with the nested card, and it erases all of the content on the card. I can reproduce this one pretty consistently.
Today I got excited because I had specifically asked the agent to change a nested card into a call-out block, and that actually worked. Based on the fact that it erases nested cards, I thought maybe it can’t read them and doesn’t understand those types of objects at all.
I've just learned not to use nested cards until the very end, essentially working in a flat structure, and then, once I'm done editing, move everything so that it's nested. But it's pretty annoying because then it's just harder to read through cognitively with such a flat structure.
I'm trying to remember, but I think I also today tried to make an edit on a nested card, and it did that improperly. So it seems to be a problem when it should not touch it specifically. But it's late, and I've done so many things today that it's getting mushy. I haven't worked like this for a while since I've learned not to mix agent and nested cards.