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.'
Source