What is the difference between deleting and disabling a mod?

Disabling

Marking the mod as disabled in the mod manager.

The game will provide a pop-up warning if the savegame is re-entered after disabling the mod. In most cases, re-entering a save after disabling a mod that save relied on will permanently damage the savegame.

Deleting

Completely removing a mod from your machine by either clearing the reserve space or manually deleting it from the console.

The game will provide a pop-up warning if the savegame is re-entered after deleting the mod. In most cases, re-entering a save after deleting a mod that save relied on will permanently damage the savegame.

In-Game Manager Options

The in-game mod manager gives you options for deleting or disabling all mods in your load order.

Return to the main menu to refresh your plugins after using either option prior to downloading anything else to ensure the system refreshes as it should. A cache clearance is advised.