What @SimsLady2000 said about MCCC -- taking out the mod could mess up the game depending on what settings you messed with.
Another way you could do it is a "clean folder install".
First, back up the folders you want to save -- saves folder definitely, and also Tray if you have a lot of houses/Sims you've created or Gallery content you've saved. (It's also a good idea to back up those two folders frequently, just in case something goes wrong with either the game or your computer. They don't take up much space unless you have a huge Tray folder, so just a little flash drive should work fine.) If you're still going to use MCCC, make sure to also backup your mc_settings.cfg file -- that way you don't have to manually reset everything.
Then, in My Documents/Electronic Arts, change the name of The Sims 4 folder to something like Sims 4 Old.
Start the game; the game will generate a new The Sims 4 folder in My Documents/Electronic Arts.
Quit without saving and go back to the Electronic Arts folder; you'll see the brand new folder plus your old one.
Move your backed up saves and Tray folders into the new The Sims 4 folder, and redownload/install any mods you still want to use. You can then delete the Sims 4 Old folder.
Best practice is to check/update mods whenever we've had a patch; there's usually a post over in the Modding/Custom Content forum that's organized by the awesome @luthienrising B) Script mods almost always need an update (though if it's mostly adding content, like the recent skin tone/Hispanic Heritage patch, they'll be fine), tuning mods might not if there are no code changes that affect them. Just hold off on playing until your most important mods are updated -- for me that's MCCC and UI Cheats Extension. (I use the waiting time to build/remodel or to create new Sims or give older ones minor makeovers in hair/clothing.) Ditto if you use CC (like skin overlays, custom hair, etc.) which is why I'm holding off on that sort of CC until I know there'll be no more game updates.