A little confused about the story

The ending of 3.5 has a relay of all the CHs protecting the coreflame of world bearing in a relay with the last of them being hyselins.

Then we're interrupted by evernight in 3.6 who wants us to bring in era nova to her liking. During the quest to stop her we find nameless titan. And finally we stop her and can bring in era Nova.

So can someone explain why do we start back in aedes elysiae and slumber for a thousand years when we should've already entered era nova?

What am I missing in understanding?