I had this problem actually! For me it was just the part where the mods would show up in the mod manager (vortex and bgm both) but when I went to load my save it would just show me a popup saying that ALL my mods were no longer installed. Checking modsetting.lsx showed everything was installed just like the mod manager said. In order to fix it, I spent about six hours disabling and reenabling every mod I had (over 300 of them by now...) until I figured out which mod was making it happen. No idea why but it was acually this mod (https://www.nexusmods.com/baldursgate3/mods/2975?tab=files) that was making the game for some reason not register any mods installed. No idea why that was, but the moment I stopped using that one, I haven't had the problem anymore.