I don't know how ponies eyebrows work.

[Sepul-Coloratura 762]

① These two pictures are quite self explanatory. ▲

② But this one with applejack's eyes, I don't see her eyebrows anywhere. ▲

③ In this picture, Applejack's eyebrows are there. ▲

④ Twilight's eyebrows disappear and reappear. ▲

⑤ In this one, Twilight's eyebrows aren't there. ▲

 

So, my only explanation is ponies eyebrows and eyelids move separately.

They can move wherever they want and sometimes merge completely with the eyelashes.

Sometimes eyebrows can move so fast and accurate, they sync their movement with the eyelashes while blinking.