FYI, Cryptic/PWE has started another round of republishing foundry missions as announced earlier today in this post. That post indicates that the republishing may fix the disappearing NPC contact bug.
They seem to have left the "playing" part of the Foundry system up. However, a whole lot of foundry missions were no longer available to play as of my search earlier today. My guess is that more and more missions will become available as the republishing process continues.
There has been no indication on how long this republishing round will take so if you find your Foundry mission suddenly missing from the Foundry search, keep in mind that republishing may be the reason for that.
Nope, not fixed. Testing my foundry mission, the npcs don't seem to disapear. However, the 5 enemy groups on my ground map only, do. Some will just fade away in the middle of combat, some will beam in and then out again and in again as a new group, and others will just appear as 1 character who runs at me and then fades away to nothing. In all of these cases, once the ALERT passes me by, they count as kills. While this is kind of cool, it doesn't work with a "repel invaders" mission aspect.