There is no definite link between the arcs. Just hints and bits and pieces.
One small but interesting one i encountered in the new game. When you find a diary in the Blighted village and read it, it triggers the first of Shadowheart strange "magical" reactions, with her hands shaking and glowing. You also find a skeleton with ancient Shar helmet right there. And in the few written pieces of info the hiding Thay wizard kept you find that a group of "dark knights" visited and even attacked the village. Which very well could be dark justicars which... went into the Underdark, and so on. Then there are the paintings in the Grove of Druids and Selune fighting the dark - Shar forces. Then the desecrated Selune temple. And on and on.
I dont think we would get so much pointers toward Shar if she wasnt involved. And if she is, she is running things. She is a major primordial diety, not just another god and has used the dead three for her own ends before to kill Mystra no less and cause a whole sundering of the Universe. And she represented herself as another god, which i already said. The Ilsensine god of the mindflayers is said to just appeared out of nowhere at one time, after a duergar uprising that nearly destroyed them completely. What a coincidence.
The land used to be under Shar's control centuries ago before the Druids/Selûnites showed up. The Druids defeated them. Then Halsin did something stupid which caused the Dark Justiciars to attack again. The Druids + Harper helpers "defeated" them again but not before the leader cursed the area around the Moonrise Towers. That was about a century ago. That's less or more the story on the Grove murals and a few books/notes found in the Grove.
That's just background information about the region and it gives insight in the motivation of certain NPCs like Halsin. It all pre-date the Absolute by like 100+ years.
