One of my outbound flights "magically" disappeared as well. It is/was out of LAX:
Malaysia Airlines 9211 --- LAX-HKG, on Sept. 27 at 1:00am
My flights originate in LAS and the LAS-LAX and LAX-LAS flights are on AA. When I booked them, the entire itinerary displayed on AA.com and now only AA flight do.
Not too worried though since others are getting positive responses out of Cheaptickets.