You are correct, apparently I didn't read my 3e lore closely enough. In ancient times, the Shadovar escaped the destruction of Netheril by fleeing into Shadow. They returned in the Year of Wild Magic (1372 DR, the 'current' year of 3e) and found their old empire buried under the Anauroch desert. The 4e campaign guide is a little vague on what caused Anauroch to stop being a desert, saying simply that "Rivers now flow from the melting glaciers, rain falls, temperatures are moderate, and in some places vegetation is particularly lush." Reading the description of Anauroch in the 3e Forgotten Realms campaign setting it is still described as a desert and the City of Shade is described as having re-appeared 'early in the Year of Wild Magic' but with no mention of the desert climate starting to change. Apparently these changes are something that happened in the intervening 100 years between 3e and 4e, which is why I (incorrectly) assumed the climate change was part of the merging of Abeir and Toril.
I haven't completed the Sundering Novels yet, I'm partway through book 5, but so far they've all been focused on agents of Netheril attempting to advance Shar's plans to take over / destroy the world, as well as gathering more power by collecting the various divine shards spread out through the various Chosen (apparently every god and their brother have a bunch of Chosen wandering around, so much so that at one point a Netheril wizard was able to establish multiple 'concentration camps' with thousands of potential Chosen at each camp.) Various hints so far lead me to believe that the Shadovar will be defeated / destroyed. Sakkors has crashed to the ground and been destroyed, for example.