Put the summary of the bug you're having here

EnderCrystals on each side of the exit portal is still exist after EnderDragon respawned and one of the crystals in the circle didn't reappear.

Steps to Reproduce:
1. place one End Crystal on each side of the exit portal at any one of the three blocks of that side
2. save and quit to title(I am not so sure)
3. get in the world again
(the dragon was killed by command kill @e[type=!Player] last time.

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Update: Endergradon respawn is frozen after exit and reload the world.