If you have loaded trains, and either reduce the number of trains on a line, or delete a line - all goods are lost (this is expected). The bug is the destination is not updated as to the loss of the delivery. They still say x number being delivered, but they never arrive (due to being lost with the train).
I am overloading trains, 799 per train, with growing delays between stations. I upgraded to larger stations, and put in 2 parallel rail lines from different platforms on each station. then made 2 lines, one on each platform between the same 2 stations. remove / add track to put all one line on one track, and the other on the second one. The bug is all freight goes on one line, (the first one created) still 799 per train, and the second line is 0. It appears that when cargo gets to a station, it picks a line, and is stuck with it until unloaded. Even if another train to the same destination arrives first, the cargo sits there waiting on the first line.
I have several stations going from point a to b ,c ,d ,e. I have 1 line with multiple trains going from a,b,c,b. and another a,b,c,d,e,d,c,b. All freight gets on the same line (the first line created) and rides from a-c, then changed to the other train at statin c to go from c-d or c-e.
I saw this by clicking on a truck heading to the train network, and watching it continue until delivered. In some cases 2 trains came and went on the line it ended up taking before it loaded. Both before and after tracking the truck the trains on that line showed 799 per train leaving that station. Trains on the other parallel line appeared empty at the time, as well as showing 0 before and after tracking the truck.