As information: the manifest does not carry the name of every single passenger on board. Names are listed for sleepers, mobility impaired, lower level, and so on. But as for plain old coach passengers, it's all just numbers.
Conductors know their responsibility of keeping an accurate record and count of the number aboard the train. There are many "home made" record keeping devices out there, such as forms that someone made up at one point and then xeroxed for others to use. These forms are usually unique to each train and/or crewbase and may take the form of a simple list, matrix/table, or whatever else. In the case of LD trains, when the train is handed over to the next Conductor, he usually takes the numbers off of the previous form and puts them onto his own, and so on.
The manifest is only good as of the date and time it was actually printed. It may very well go out of date before a train even leaves its initial terminal, due to last minute bookings/cancellations. Updated manifests can be provided at any station with an agent on duty, but at times, those can be many hours apart. As a result, to many crews the manifest is mostly seen as a planning device (how many people and where to put them?) as opposed to a record-keeping device.
Now, when enroute changes to the manifest happen, the Conductor is technically supposed to inform someone with ARROW access, so that such changes can be entered into the national system. Such changes might include: bad orders; sleeper rooms swapped for convenience or by request; additional passengers show up at a station unexpectedly, but are allowed on the train since there is enough room; and many other situations. Even with the advent of railroad supplied cell phones, getting these changes put into Arrow is a time consuming process, and there are many areas where cell phone reception is not available. So a Conductor has to keep a running tab of the changes and then report a bunch of them at once.
Before cell phones, these kinds of things used to be accomplished by little paper forms, which were dropped off at the next staffed station, and any instructions that the Conductor wrote down would be carried out by the agent. Either way, it's an imperfect system, since there is a length of time - which can be pretty sizable - during which Arrow's account of a train's passenger load may differ from the actual (Conductor's) account of same. The only thing to fall back on is a particular Conductor's own paper records.
As I understand it, regarding the incident of #5(22), those very paper records were burned in the fire.
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