i had a spirit disappear once and the same problem.
i pulled heroes out of the inn that i had sent in and switched gear with autoequip and it popped back up.
if i remember right, i just had that particular spirit upgraded and not restarted. i think its related to a bug that "produces" a new item while you still have the old item until you refresh. if you use autoequip you will see the new item on the next hero but in reality it is still on the old hero. if you then send the old hero into the inn right after, the newly crafted spirit will go with it.