When an update happens to the game, mods may stop working.
If it is a interface mod like armor and quickslots, you may have to wait for an update for your stuff to show up in the game, it's not missing, it's just not visible.
For functionality mods like epic loot, you can just remove the mod until it is updated and keep playing without it.
For significant changes in the game, you'll have to wait for mod infrastructure to update (bepinex).

You can always remove the mods with your mod loader - or manually, just don't remove the mod config file or you'll have to set your mod settings again. This will allow you to play normally on your save until mods have been updated.
Many mods don't need to be updated unless the underlying code in the game gets an update or there is a big change to a library the mod depends on. Those should work between updates.

As always, being a mod user means that you will always have to deal with this inconvenience and learn to get along with it and overcome any of the challenges it presents.