Can someone explain this?

[FCIN]

So let's say they get the stopped train moving again, and no train has come up and exploded the torpedo. Does someone have to get that torpedo off the track, or do they leave it there?

They would be left where placed. This protects the flagman as he walks back to the train and gives the train time to get moving again. There is no provision in Rule 99 that requires removal of the torpedoes, or extinguishing fusees. Would sort of defeat the whole purpose, as a following train could over take you before you got back to the train.

Any following train that encountered the torpedoes/fusees, would be required to follow the rules (stop and proceed at restricted speed in most cases) and could not resume normal speed until it was known that the route was clear.