Simple step by step guide that works. First subscribe all the mods you want or might want, and mark them as favorites in the workshop just for convenience.

1. Make sure cloud storage is on for this game and have downloads while game in progress turned on in steam settings.
2. Open file manager and find Users(your name)\Documents\ParadoxInteractive\CrusaderKingsII\Mods
3. Delete all mod files located in that mod folder.
4. Start the game launcher. Your subscribed mods should now redownload and appear in the launcher but wont be selectable yet.
5. Close the game launcher.
6. Start the game launcher. Now all your subscribed mods will be there and selectable in the launcher. Check the mods you want active and start playing.

Thats it.

If you need to add or remove mods later you can repeat these steps to clean up the mess.