Mods are certainly more difficult than they were - I don’t believe this is actually due to the upgrade itself, but rather a result of Funcom’s launcher being broken for this feature and Funcom having little impetus to fix it, since they are no longer responsible for developing the game (essentially, I suspect there is a little bit of a ‘territorial p*ssing contest’ going on - Inflexion can’t fix the launcher, because it’s Funcom’s launcher, but Funcom doesn’t ‘care’ because it only affects a game that is no longer ‘their problem’…).
(An additional factor is that with the upgrade, we lost access to CodeMage’s excellent BUGLE launcher, which did so much of a better job than the base Funcom one ever did, especially for swapping modlists around.)
Possible reasons aside, there is a way (at least for singleplayer, but probably also for servers) that we can make this process easier for ourselves:
Navigate to the ‘Mods’ folder (by default - C:\Program Files (x86)\Steam\steamapps\common\Conan Exiles\ConanSandbox\Mods)
There should be a file called ‘Modlist.txt’ (unless you have no mods currently in use - this will work better if you get a modlist set up correctly for one of the destinations that you intend to play).
If all of the places that you wish to play have the same mods in the same order, and just have some additional ones, then it is possible to ‘comment out’ the unwanted ones by adding a semi-colon at the start of that line - then reactivate them by changing the textfile when you want to go to the other list.
Assuming that the lists are too different for this to work - create another folder on your desktop and copy modlist.txt into that folder (and add something to the filename to make it easier to identify - eg the server name or character name).
Then go through the song and dance of setting up the second modlist correctly - and create a copy of that modlist in the same folder (and again, add to the name).
Then, once you have two modlists that each feature the correct mods for those games, in the correct order - manually swap those files in and out of the ‘mods’ folder as needed (remembering to change the name back to ‘modlist.txt’ when they are ‘active’).
(In fact, you could probably just keep them all in the ‘mods’ folder, since the game will only look for ‘modlist.txt’ and will therefore ignore ‘bobserver modlist.txt’, until you rename it to be the active one.)
This way, at least you only need to exit the game once, swap the file, and restart the game, rather than having to go through the extra steps the game currently enforces.