No idea about what happens with a breakdown though I can't imagine why it would matter with a train as the readers are at the station not on the train. But, Presto copes all the time with multi-segment, multi modal trips. It even copes with, for example, a trip involving two different transit authorities so if one takes a GO train then an Oakville bus it calculates the lower combined fare regardless of which comes first. I have been using it for three years and have not had a single problem other than TTC buses showing up with no reader or the reader not working.