There's a lot of speculations in regards to the tree with Bran that I've already seen, including theories that, "...but you will fly," implies Bran warging into a dragon. When I saw this theory, I wouldn't be surprised if that's why they set up Drogon mysteriously disappearing for days.
Spoiler
Honestly if you didn't predict any warging into a dragon by the middle of the second or third season you're an idiot. It makes even more sense now because the most vicious dragon, the one that burned the child and goat, is missing, which would tie in perfectly with bran's appetite for violence when warging if he does end up warging drogon. I think it's sad that khaleesi detained the two "harmless" dragons in response to the missing violent drogon having killed a human. I hope that doesn't come back to haunt her later.