It's usually a common mistake that I have is when i using call stabled pet, sometimes pets disappear from the list, but it does not matter because when using that empty space it reappears
But now I lost a pet, it was skoll to spiritual beast ... I tame it today, when I finished , I put it in the barn using call stabled pet and changed specialty to MM, time later, when I wanted out, I changed to BM , but it is no longer there, it does not appear in the list, i wait a long time to be able to tame it.
Actually they are not disappearing, just stacking in 1 slot.
Take a diffrent pet from stable and try replacing it with each stabled pets 1 by 1.
You will find your precious Skoll