Thinking now fatigue never really does go down like damage, which can be repaired. Fatigue a reflection of hours flown? Still sure I remember resting units at sea and plane fatigue going down, just seems really slow at a base with more support.
Changing AC types at the base always helped repair all the new types faster than on board ship. May just train em some more till they almost fall apart in obsolete frames, then upgrade for sparkling new planes before deploying.
I think of damage as what front-line mechanics and sheet metal guys can fix day-to-day. The Fatigue tab shows deep, accumulated damage to the airframe and engine. To get rid of it the plane needs depot or IMA-level work. Tearing the engine down to the block and rebuiilding it sort of thing. Not the kind of repairs that could be done on carriers at sea. The game will let this happen, but it's slow, and it should be.
My experience is aircraft fatigue will go back to zero, or low single digits at least, but it can take a month or six weeks. Usually not worth that. I rest and knock fatigue down into the teens, then send them back up. Risky? Yes. So is not having planes.
As in so many cases, this decision is left up to the player. There's no right answer, and the answer might be different in 1945 than 1942.