With Island living coming next week.......

Moving them to your desktop before you install is always a good idea. Then you can move them back once the game is loaded.

Just move them out of your mods folder and see if any needs to be updated. Usually people post a list of broken mods or mods that are no longer needed as it's been added to the game itself, etc....installing with the mods is probably fine; but it will affect the game if you try going into the game with broken mods. Patches always break things due to updates and changes in the game.