Will you be in a sleeper compartment or in the seats? I don't know what the situation with the seats is; but in the sleepers it varies as to whether they take your ticket or not. They likely won't even want to see your passport as long as you are staying within Schengen, let alone take it. If they do want to take the ticket I suppose you could ask them to wake you instead (though the people you are sharing a compartment with might consider this rather anti-social).

Could you be more specific about the trains you are taking, we might be able to give you more detailed avice that way.