<i>Flight to Paris, train directly to Brussels, and at the end, train from Brussels to Amsterdam, flight home from Amsterdam.</i>

I can understand that part of a flight cannot be thrown away without the rest of the ticket being cancelled, but how would an airline company know that the train ticket was not used?

Yes, she'll have to.

<i>Yes, she'll have to.</i>

That does not provide an explanation of how a train ticket is linked to an airline ticket just like another airline leg.

The combo is actually sold by the airlines and the train trips are treated exactly as if they were other legs of the air tickets. They are completely tied together as a package. If you skip one segment, the remaining segments are cancelled. Sometimes it is a good way to go, cheaper than separate tickets, if it is going where you actually wanted to go. In this case, the OP took the cheap package, not realizing the limitations. She checked with the airlines when the question was brought up by another poster.