Twice in the past month I've had chickens underground, in a fenced in area, that disappear when I go to the surface and return.  Both were well lit areas and were fenced in, nowhere for them to go.   No feathers or chicken meat laying around either. 
Both times the chickens were captured after being ridden by baby zombies.  I believe that the chickens are being treated as a mob, if you leave them alone for a period of time they disappear.  But I'm sure that in the past under older editions I've done this and the chickens stayed around after a baby zombie was knocked off of it. 
Solution would be to have chickens that are spawned with a baby zombie to be treated as normal chickens and not as a mob.
Thanks for looking into it!