If Shawn's suggestion doesnt fix this ::

I would first --> disable ALL the Fade options for the lens flares in your scene (hoping it pops back to active).

Then, If that does re-activate your lens flare visibility  - then unhide everything in your scene -- layers , objects and whathaveyou  -- and try re-enabling your lens flare HIDE options w/evrything active in scene and make sure you're okay as you tick them on, one by one.