@ihaveonecat ivy does this occasionally. When she was taken into the rescue she had cat flu, she was over it when I adopted her but then 6 months later she was poorly with sneezing, head shakes, holding one ear really flat and growling if I tried to touch it.
The vet said she had a virus linked to the cat flu (can't for the life of me remember what he called it) and it will recur over the years, she just needs a steroid jab every time.
Could it be something like that?