What is the difference between a 'clean save' and a 'vanilla save'?

Introduction

There are two types of 'clean saves'. One is actually a vanilla save, the other is a bad modding practice in an attempt to re-initialize a badly scripted mod or an updated mod that doesn't use version control to initialize its scripting when a user updates. Or the modder doesn't understand about persistence and doesn't realize that you cannot update some mods in the middle of a game.

Vanilla save/Clean Save

No mods enabled.

Clean save

Also known as re-initializing a mod and is only used if a badly scripted mod stops working or a mod author has not included version control scripts to reinitialize quests and scripting.

It is not advised on any platform to disable a mod and continue on the same save. Due to persistence and other issues, most scripted mods cannot be updated in the middle of a game.

Additional Reading

Levels of Persistence - Mostly Skyrim related but contains information about Fallout 4 as well.

Creation Kit Technical Information: Save File Notes



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