BG3 Mod Manager can technically still work with a little copy and paste action as well as pinning folders to quick access in Windows Explorer for ease of navigation. It's a bit of an involved process, so I'll try to explain it as simply as I can. It may be possible to use Vortex to follow a similar process as well, but I don't use Vortex so I can't really say how that would work.
Start by going to the Documents > Larian Studios folder, wherever that is located on your PC. Right click the Baldur's Gate 3 folder and hit "pin to Quick Access". This gives you a one click button to navigate here from any Windows Explorer instance. With this out of the way, we need to make a copy of your Mods folder, which if you've launched the game with the Patch 7 update, the game will have straight up moved the Mods folder from the original Documents location to the new one over in AppData. You can find it by going to the top bar of your current Windows Explorer instance and typing %AppData% and hitting enter. Once you get there, back out of the Roaming folder and you'll want to go to Local > Larian Studios and once again pin the Baldur's Gate 3 folder here to quick access as well. Until an update for the Mod Manager is released, you'll want to maintain identical Mods folders in both locations for reasons we'll get to shortly. Just remember the old one is on top and new one is on the bottom.
From here you just go into this Baldur's Gate 3 folder, and this is where your Mods and Profiles will now be located. The Mods folder was moved in its entirety, while your profiles were just copied. Now you simply need to copy the Mods folder, click the first Baldur's Gate 3 folder you pinned to Quick Access, and paste the Mods folder back in here so the BG3 Mod Manager has something to work with. From here you can just use BG3 to export your mod list to any profile as normal, ignoring the error message because it didn't stop what we needed to happen, it still generates a working modsettings.lsx file. Once you have done that, navigate to that profile in Explorer, copy the moddsettings.lsx file, then paste it into the appropriate profile in the new profiles folder, which you can get back to easily with your second pinned Baldur's Gate 3 folder. You now have a working modded profile.
It seems like you may have to do this every time you run BG3 with mods now though as it worked fine for one session, but I was getting a warning after completely shutting down the game, launcher and all, and then coming back later. I was getting a pop-up warning that said all the mods in my current profile had been disabled. Exporting the load order again with BG3 Mod Manager and copying it back into my active profile before restarting the game made this pop-up go away. I didn't try loading the save without doing this, but it's probably safe to assume the mods wouldn't have been working anymore just like it warned me.
One caveat, of course is that ImprovedUI is currently broken, so you need to remove that entirely from your mods folder. To get past the glitched window that will be hidden behind character creation without ImprovedUI, just hit enter as soon as you fully load into chargen and it should close. I also don't know what other mods might be broken by Patch 7 so you'll have to use trial and error to figure that out yourself.
Cheers and I hope this complicated process helps people get back to playing BG3 with their favorite mods in the interim of a better solution.
Edited by Keth, 16 February 2022 - 11:29 PM.