A break-in-two means the train has broken into two (or maybe more) sections, usually because a coupler knuckle breaks -or more dramatically, the entire drawbar pulls out of one end of a car.
This happens as the result of slack running in and out as the train accelerates, decelerates, and travels over changes in gradient. As trains get longer, the slack action is more pronounced. It's a major concern with trains now approaching three miles in length. There is a small amount of slack between each car, so when the trains are longer the cumulative slack action is greater. It's quite common for one end of the train to be speeding up while the other end is slowing down.
Primitive automatic locomotive "cruise control" systems may control speed as measured by the locomotive, but it takes considerable intelligence to be aware of the gradients and brake action and anticipate what the slack is doing throughout the train. No two consists will behave identically, because the brake and draft gear performance on different trains made up of different types and numbers of cars of varying weight will vary every time. Application of throttle and brake has to consider the slack and potential run in/out.
The point made in the article is that the newer systems are capable of more of this this. Without this intelligence, a human engineer is likely to run trains more safely than the computer - but it's a very mentally tiring task and requires constant concentration, so it's desirable to automate if it can be done reliably..
By the way, when a break in two does happen, the air brake hoses separate between the cars and this throws the train into an emergency brake application. Not only is this a mechanical breakdown that immobilises the train, but the emergency stop will create its own slack action that can jackknife or derail cars, or break additional knuckles. So, an event to be avoided at all costs.
- Paul
PS - why does the knuckle break? It's designed as the weakest link in the train's draft gear. Better a broken knuckle than damage to the draft gear or main spines of the cars themselves. Even so, a knuckle weighs up to 100 lbs, and getting a spare from the locomotive (they carry spares) to the broken coupler, and hoisting it into place, in the middle of nowhere, is a slow and quite unpleasant task - especially in rain or snow.