Eternal Nightmare doesn't stay dead on leaving the area/instance reset

After killing the three guardians and using the organs to open the black core, I left the area to do a side quest. Upon return, I needed to kill the guardians again. Instance had reset but did not save the fact that i opened the black core.

Ref # 391,714,708

That’s not a bug. You have to kill the guardians each time you want to enter the black core. It should have been in the message you got when you clicked the door that there were still guardians alive.