Force Steam and the game to re-download all workshop content:

-Go into your Steam directory and find the workshop folder for DOS:2. The path should look something like (C:)\Program Files\Steam\steamapps\workshop\content\435150
-Delete the 435150 folder. Make a backup if you're nervous, but it's not necessary
-Go to Documents\Larian Studios\Divinity Original Sin 2 DE\Mods, and delete everything inside
-Start the game.
-When you first click on the Mods menu option, it will show up as empty, but if you exit out of the mod menu then back in, you should start seeing the list slowly being populated as Steam re-downloads everything.
-Once the mod list is fully populated, see how many mods there are, and compare it to the number of mods you have subscribed to.

There is also a workaround where you simple copy the mods from the 435150 folder to the mods folder, but future updates of these mods will then be downloaded to the 435150 folder leaving you with outdated files.