The only area not yet clear about the chain of events that caused the Sept. 29 mid-air collision over the Amazon centers around the Legacy's transponder malfunction that lasted 55 minutes, until impact.
It is not yet known why the Legacy's transponder went off line and suddenly came back on line after impact. Had it been working as the two planes closed in on each other, it would have been the last chance to avoid the mid-air impact that had already been set in motion when air traffic control in Brazil had the Legacy and the 737 flying at 37,000 feet on a collision course.
A safety recommendation issued today by the National Transportation Safety Board summarized what's publicly known about the transponder issue. It says that the Legacy pilots were not aware the transponder was not signaling. Air-traffic control in Brasilia would have had that information on the ground, but for some reason failed to follow up.
There is a "lack of a conspicuous warning" to let pilots know that a transponder is not signaling, the N.T.S.B. said. It recommended to the F.A.A. that "existing and future system designs" for transponders and the collision-avoidance warning systems that work in tandem with them have "an enhanced aural and visual warning requiring pilot acknowledgment" if the equipment is not functioning. Here is the recommendation From the National Traffic Safety Board .
Correction: That's the National TRANSPORTATION Safety Board, of course -- but the link as posted above still works.