I feel for you! Had similar experiences and really wish old Haldor sold "Alfar mercenaries" that could guard your bases in such times. Most tame animals cant defend against the flyers at all causing hours of effort taming to go puff in <90 seconds.. Not fun.
And yes I DO KNOW we can kite the buggers away in many cases. (Lets leave aside the logic fail of LEAVING your fort to defend your "Fort" for a moment)
But in several other cases if you miss one or two they wreck your crops and animal stocks even if you got most of them away from your base where you can sledge the boogers!