That section used to be the main Santa Fe main line, but now the BNSF trans-con runs thru Amarillo, TX. So BNSF technically abandoned that portion, as the only train running on it is the SWC. There was a dispute that it would not be maintained any longer, but an agreement was reached.
Technically, it is not abandoned, BNSF has not filed for abandonment on the line ever, but it isn't used by them at all any more, at least between Lamy and Trinidad, and between Trinidad and La Junta. If they actually filed for abandonment and it was successful, nothing at all could run on it, including 3 and 4. Amtrak would almost certainly protest the abandonment petition if they didn't work some kind of agreement with BNSF in advance.
Back in the day of railroad operated passenger trains Santa Fe had the Northern mainline, which is this line, and was primarily used for through passenger service, and the Southern mainline through Amarillo, which was the primary freight line. They were both mainlines. The northern route also saw fast freights, the Super C ran via the northern line. The Chief, the Super Chief and the latter-day versions Grand Canyon ran on this line, the San Francisco Chief ran on the southern line. Before the San Francisco Chief the "southern" section of the Grand Canyon ran via Amarillo.
And the semaphores are operational. BNSF started upgrading the signals, but then decided they didn't want it any more and stopped. The line is a veritable signal musuem, with the semaphores, targets, pole line, cool old cantelievers that BNSF is rapidly replacing elsewere.