First, a bit about brakes, cabooses, and FREDs.
Brakes on Amtrak trains are electro-pneumatic. That is, while the brakes themselves operate by air, the signal that tells the brakes "apply" is transmitted electrically. This is different from freight trains, where the signal to brake is transmitted by a reduction in air pressure in the brake lines. This means that it can take a long time for the brake signal to propagate down the length of a freight train.
Freight trains used to have a caboose on the end, where the conductor and other crew members rode. One of the reasons for the caboose was that it allowed the possibility of applying the brakes from both the front end locomotive, but from the rear end by the crew in the caboose. Nowadays, nearly all cabooses have been scrapped and replaced with a FRED: a Flashing Rear-End Device. A FRED not only displays the required red marker light to the rear, but also communicates with the locomotive by radio, telling the head end what the brake line pressure is, and in some cases allowing the engineer to apply the brakes from the rear as well as the front.
Amtrak equipment generally doesn't require a FRED, because the cars themselves have built-in rear red marker lights and because they use electro-pneumatic brakes, so "two-way" braking isn't required.
Speculate for a moment that the brake circuit on the baggage car (normally at the front of the train) failed in some way. This by itself is not fatal, because you could shuffle the cars around and put the baggage car on the rear, where the lack of brakes wouldn't be significant. But baggage cars don't have built-in marker lights, and you must display markers (a red light to the rear), and Amtrak trains don't as a rule carry a FRED around with them.
Our speculation is that due to the bad brakes in the baggage car, the crew of the Zephyr had to shuffle the baggage car to the rear, but also to put one additional Amtrak Superliner car behind it to serve as "protection" with the required rear marker lights.
If our speculation is correct, it must have been very inconvenient for everyone, and I hope the train wasn't fully loaded, because probably at least one coach or sleeper (I didn't see what got shifted to the rear) had to be cleared out and the passengers moved. Or possibly they moved the transition/dorm car (which would have been easiest since it's coupled immediately behind the baggage car) and shafted the crew, at least until they could get to Winnemucca (where they might have been able to borrow a FRED from Union Pacific) or even Salt Lake City (the scheduled servicing stop).
Incidentally, the trainset that passed Fernley heading east on Saturday night is the one that arrives this evening in Chicago as train #6. It's currently expected to arrive a bit more than 3 1/2 hours late at 6:39 CDT, having lost even more time along the way.