Mystra and Shar had never been on good terms. They were both gods of magic, and the natural rivalry between the two had ensured that only one could survive.
Shar had been thought fallen in the Final War, but she’d actually managed to escape the destruction of her divine kingdom with serious injuries. Some amount of luck had allowed her to flee to the astral plane, stumbling upon the Shadow World.
Mystra, on the other hand, had established the Weave to gain the support of worshippers and other gods. She’d become the guardian of the Weave, and the other gods had moved the channeling of their powers to complement the system.
Even having become a greater god Mystra was still cautious of the Goddess of Shadows. After all, Shar was the one god that could take over her position.