Obviously the revenue management system was not at fault since the fare was available minutes later. However, an experienced agent should know how to adjust the reservation instead of making a new one (at a higher fare) and then releasing the old reservation.
The
new res must have come from the bucket
only one up from low bucket, and it was
first one out of that bucket. So once the old low bucket res was canceled, the next would dropped back one bucket. In general, the new res could have been the last one in high bucket, in which case the fare would not have dropped when canceled unless there was only one space in high bucket to start with (in the absence of manual intervention by the RM guys, of course). So in this scenario, even if the agent had known how to do a "trial cancellation", it wouldn't have yielded low bucket.
So it gets down to can the agent override the system to get the
original bucket, not just the one available if the cancellation were considered first? In cases where someone wants to change a room number from the one the system generated, the answer seems to be YES. But what about changing the itinerary, even if it's only a small change?
I'll give you another actual case that isn't quite as absurd as the OP's since "discharge only" was not involved.
I booked a roomette MTP (Mt. Pleasant, IA) to DEN. Sometime later I realized I needed to board at GBB (Galesburg IL) 2 stops east of MTP. The telephone agent wanted about $150 for the extra 1:20 ride in the roomette (I don't know or remember whether the agent repriced it GBB to DEN or simply added the GBB to MTP fare). I declined and purchased a coach ticket instead.
As it turned out, when I was getting ready to board at GBB, the conductor asked me if I would be willing to head back to the sleeper right then. It made sense from the conductor's standpoint because if we had boarded in coach, at MTP, a quick stop, we would have to drag some large pieces of luggage (baggage service had not yet been reinstated at GBB) from the front to back of the train either on the platform or through the diner at supper time.
Whether the revenue management system or the agent who is following what the revenue management system is telling him was at fault is debatable. Bottom line was that Amtrak lost the roomette fare from GBB to MTP since the chances of someone booking that space is near zero.