When freight trains were scheduled in the timetable, they were usually designated as second class or third class trains. At the top of the schedule column, just below the train number, you'll see the train's class. On branch lines where a scheduled freight train went to the end of the branch, turned, and returned, the same engine would typically change train numbers at the turning point and return under the train number in the opposite direction of its outbound trip. Same engine, same caboose, same crew. If the outbound trip was in the direction inferior by rule, then there would be a special instruction that, for example, No. 136 will not depart Wheat Center before arrival of No.135. That allowed the outbound train to be late arriving at the end of the branch. Otherwise, it would have to take siding and clear the inbound train on the inbound train's timetable schedule. But, since the inbound train equipment was the outbound train until it arrived at Wheat Center, it would have been impossible to clear itself. Of course, the schedules would all expire after twelve hours, and they could them move the train by train order as an extra. Anyway, the point is that the timetable schedule and any special instruction eliminated all that confusion and made it possible to run the train when no train order offices were open.
Now, as to actually running the train, on any day when there was no reason to go out the branch, the Dispatcher could annul the train. If there were any other trains that used track where the branch line train was scheduled in the timetable (for example, if it was scheduled to run 25 miles on the main line, then go up and back on the branch, and then go those 25 main line miles back home) any other trains operating in that territory during the time the branch line train's schedule was in effect would be given a train order that informed them that Nos. 135 and 136 of (date) are annulled.
The regular branch line crew would stay home and mow their lawns. Or go fishing. 
