I have a AA flight scheduled for Nov. 28th from Chicago to San Juan. I plan on waiting a couple of weeks before I call the airline. From what I understand, American Airlines will re-schedule passengers effected by the pilots calling in sick. I'm not worried because I booked through the airline. If I were in your situation I'd call the travel agency to see what options (if any) are available. Usually these types of problems don't last long with the airlines.