Im running your latest build with the latest version of paper.

I deleted the world folder for the end to regenerate the end. Now we cannot kill the dragon because it disappears and then respawns with full health. We can see the dragon disappear and then it takes about a minute before it returns. Maybe this have something to do with the respawn/heal feature of this plugin, even tho I have this turned off.

This is my config file:
http://txt.do/d90v5

I have one console error but i don't think it related to this bug since it happens before (the bug happen right before I wrote /gamemode 1.)
Console error:
http://txt.do/d90vr

Is it possible that this has something to do with the rename of the enderdragon?
From EnderDragon to Ender_Dragon.

http://minecraft.gamepedia.com/Ender_Dragon#History
https://hub.spigotmc.org/javadocs/spigot/org/bukkit/entity/EntityType.html#ENDER_DRAGON

Is it possible that this has something to do with the rename of the enderdragon?

Minecraft name changes != bukkit enum changes.

I don't think bukkit changed the name of the entity.

Alright,
do you have any thoughts on what could be causing this bug then?

Hm I think it has something to do with the looting tables, they all woks (no error on startup). But when I removed them it seems that the dragon works as normal. Bug might not be related to this plugin, but perhaps minecraft/bukkit itself.

Before this happened I also gave the dragon a custom name. When it respawned it still had the custom name, but with full health.