2003 Ford Taurus Starter and flywheel

My Girlfriend has her car in the shop as designated by her "extended warranty co." They say it needs a new flywheel and starter and must do the flywheel before the starter. Warrnaty co. Says flywheel would not be covered (seems strange). Repair shop says flywheel cost for part is minimal but labor is approx 6 hours to do the flywheel job. If we take the car for a 2nd opinion then the shop will charge a diagnostic fee once its taken off the lot. What questions do I need to ask to be sure the flywheel needs replacing, and what should I reasonably expect to pay for this work. We live in Elmira, NY (upstate).

Thank you.