From serebii:
>As you progress through the Delta Episode, you will eventually come to a climax which has you and Zinnia reach the top of Sky Pillar and awaken Rayquaza. Rayquaza eats your meteorite and refuses to accept Zinnia as its protector, and instead wishes to challenge you. It's at Level 70 and requires capture to proceed. It also will require you to send a Pokémon back to your box from your team. Immediately after capturing it, Zinnia teaches it Dragon Ascent and challenges you to a battle. It can Mega Evolve without holding a Mega Stone, but needs to know Dragon Ascent to do so.
So if Rayquaza starts to shit out that meteorite it wont be able to mega evolve again, right?