Hi! I see I’m not the only person with this issue … but I’m not finding support on it, so I wanted to make note and see if anyone else has ideas of a fix.
I flew up to Pepe … he disappeared in my Garrison … I saw the note “you are mounted” and now he’s just … gone. no buff. no respawn. etc.
Help? 
The respawn in your garrison should happen within five minutes. If it doesn’t, try leaving your garrison and go back. If it still doesn’t, try logging out and back in. You may need to reset your UI.
You can’t fly to get him on most classes. You need to get him from the ground.
There are a bunch of suggestions there for getting him from the tree.
This page has all the cosmetics to go with your Pepe.