Im a lot confused. Is Explore the note a Continuation of the Lost Tomb (The one with Chen Yi). The Ending of Lost Tomb 2 and Explore the note seem to overlap story-wise and setting c=wise.

It is a continuation!

They reveal to us what happened after the tomb      collapsed on them and what Wu Xie discover before  going to Changbai mountain. In The Lost Tomb 2  they are showing us some hints but not the whole picture.

But at the same time it's not...

Now that I'm rewatching The Lost Tomb : Heavenly Palace in the Clouds i can see that Wu Xies mentality is a little unstable, he feels betrayed and he can't stop overthinking  about the situation he's into. If you compare the two seasons you will realize that Wu Xie as I mentioned above is different he does not trust anyone except Zhang Qiling and Wang Pang Zi but he is still determine to find out the truth about Wu San Xing and Xie Lian Huan and the Mystic Nine.