1. The TGV will arrive at Basel SBB station, from where the IR 27 service to Lucerne will depart, too. The change will not take more than 5 to 10 minutes, depending on the amount of baggage you will carry.
2. If the TGV is arriving late, yes, you would have to buy a new ticket since the entire trip is not booked all in one ticket. You can ask for a refund of the Super Saver ticket in that case. Buying national Super Saver tickets is not a good idea when arriving from international destinations, neither is it a good idea when arriving by air. However, TGV services are usually very reliable, apart from the days where they the staff is on strike; a 50 minutes transfer is sufficient and well doable.