Thought I replied to this, but I can't find my post >_>
Oh well, will make it again.


The relic quest line is built on shaky lore.
I'm pretty sure canon doesn't allow us to kill the Primals (HM) more than once.
Though you could say we happened to be on the quest when the primals came back for the second time.

But then we have the books which ask us to go to the NM versions of dungeons that have a HM.
That's going back in time, technically.

Most of these type of things get explained by us reliving memories.
This happened with Savage, Ultima EX or the Crystal Tower weekly quest.
The Primal Focus weekly didn't even bother.

The Relic had too much to really try so it's best not to try to fit the details into canon.
It's more like reliving heroic deeds of past heroes or sometimes forging your own. The context isn't given, but it should be assumed there was some.

And stuff like going to Normal Mode dungeons would need to be overlooked.