This article discusses the importance of “cleaning” plugins.
The process of “cleaning” plugins by undeleting and disabling references and removing ITMs can be controversial. It has been recommended as a basic step at the start of building a setup, often by people who do not fully grasp what “cleaning” does.
Cleaning addresses the following potential causes of problems:
The official master files contain various deleted references and ITMs which, according to Arthmoor, will cause issues:
Arthmoor specifically refers to “dirty edits” (ITMs) which can occur very easily in the Creation Kit. Though I know of no specific example, an unintentional ITM from Dragonborn.esm that overwrites a vital change in HearthFires.esm can very well break the game.
However, Arthmoor also implied that the USSEP fixes those instances. Although this is circumstantial evidence, I did not use cleaned masters in several years (and therefore users of my Wabbajack lists did not either) and no issues were ever traced back to uncleaned plugins.
Plugins added by mods can also have deleted references and ITMs. It is generally considered good practice to clean plugins before publishing them and the presence of these issues can be an indicator of sloppiness in the creation of the mod.
Nevertheless, I would not consider “cleaning” plugins from mods an essential step in building a setup. While it is true that ITMs can overwrite crucial edits from other plugins, such cases would create obvious conflicts in SSEEdit that you would be expected to check for and address anyway.
As with the official master files, I have yet to see an example of a mod where “cleaning” fixes a specific issue.
I would not generally recommend “cleaning” plugins for the sake of it.
Undeleting large references is a prerequisite for DynDOLOD NG, so you should clean plugins if you intend to use that. At the very least you need to make sure there are no deleted large references.
ITMs can sometimes cause unintentional conflicts, but those will be very visible in SSEEdit when you do your conflict resolution so you can address them then.
It is unlikely that “cleaning” ever breaks anything, so there is nothing wrong with doing it. For the most part it just does not fix anything, either. Like other common practices in the modding scene, it is generally misunderstood and overrated.*
**I am referring to those YouTube videos promising to fix all your issues and turning your modded setup into the smoothest possible experience - and then simply clean the official master files. No, this will not magically fix everything.*
(Intentional ITMs: Some mods warn against cleaning because they claim to require an ITM, i.e., they require a vanilla record to be in its original form and not changed by other mods. It can be convenient to keep the ITM, but removing it also does not break anything as long as you ensure there is no unintentional interaction with another mod.)