Aside from summoning him at night, there is a bug in which when the player summons the boss at too much of a height, the boss will fly off screen just disappear. I would suggest summoning him with the mechanical worm at a lower area and, if the attack pattern makes the boss go towards the sky, not to follow him with wings. Again, if the boss goes too high into the air, the entity simply disappears. (I believe this is a mobile only bug, as well.) If this is not the case, it could be a bug that the Terraria Devs would like to see. You may want to submit a bug report to them.
EDIT: I did do a little research on this, and besides the glitch above, where the boss despawns when too close to the border, I found this on the wikia:
On mobile version, if you fight The Destroyer near the edge of the world and his head goes out of the world, the head will be replaced with the nearest mob. The Destroyer's body will follow the "head" and after a little while, the Destroyer will die with no death message or drops.
There are a couple other bugs which cause the Destroyer to act oddly, you may want to check the behaviors of the bug.