Having two tix booked so as to avoid minimum stay requirements is a violation of the ticketing rules, and the carrier can refuse you the miles, refuse to carry you, try to make you pay the "real" fare, or cancel your FF account. While others are correct that you are not likely to get caught if you do it infrequently, you probably will if you do it a lot, and that defeats the purpose of earning the points in the first point.

To the OP, you will definitely not get the points for the throw-away segment(s), regardless of whether you have checked in online or not. If you're not on the plane, you get nothing.

S.