Currently if you summon a new dragon in a END world if that dragon is killed this not generate a new end gateway or the exit portal (if was destroyed). in teory this issue is because custom dragons not has a dragon fight instance where this things are handled.

Steps:

• Join to a end world
• if has a normal dragon kill with commands (or use a END with already killed dragon)
• Summon a dragon (summon /summon minecraft:ender_dragon)
• Kill that dragon normally
• End Gateway and exit are not generated