The flap track fairings are not obligatory for safe operation of an aircraft.
I found a post on Airliners.net, regarding a B757:
Straight out of the MEL/CDL manual for the 757, The item falls under CDL 27-51-1 which states there are 6 installed [Flap Track Fairings, Remark] on the aircraft and up to one per side may be missing. No fuel burn penality but there are a few small weight penalities, no speed penality. Our A-300's with the same CDL item does have a 1% fuel burn penality and only one can be missing out of the 10 installed. I see this item come up 3 or 4 times a year, no biggie.
However, some Newspapers overact such things a little. It's about the loss of a flap track fairing on a 737 by the dailymail.
Pilot tells 109 passengers on plane that part of the wing had 'fallen off' and is then forced to make emergency landing
Lorenzo Hernadez Jnr took to Facebook to speak of what he described as his 'near death experience.'
'I heard a few people to the side of me scream to the aircrew, a piece broke and flew off and a panel was hanging.'
He goes on to describe how people were 'praying' as the plane experienced 'the worst turbulence ever.'