It's an issue of distance. I've confirmed this in multiple Foundry missions. If you move a certain distance away from NPCs (allies, enemies, or contacts) they simply disappear. This is especially obvious in space battle missions. Fly a little ways off and everyone disappears. Try it. It's happened in every Foundry mission I've played today.
If what you say is true, I bet this has something to do with the new ability to despawn enemies and NPCs. Before they couldn't be hidden, so they were never hidden. Now they are hidden automatically by the engine at a certain distance.