I also had an issue with one of my Dragons today. I had a Royal sitting in my booster bank, and after finally getting stone walls up on a 2nd city (Annuminas) I deployed it there. I had the population cap and everything, but the dragon just disappeared without a trace. Never spawned on my land, but from the World Map view I could see it listed in my Hometown troops. However, after logging off, it was gone forever.
I'd like the influence or dragon back, any help is appreciated
I still have my Red and Haunted on my 1st city, and haven't had an issue, perhaps it's contained to Royals only.