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Discussions Rules and Guidelines
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It is ok to clean mods that LOOT says should be. But to go through and attempt to clean every mod will be just a waste of time and you could possibly clean edits that the mod needs to work correctly.
ITM's may sometimes need to be cleaned, but other times the mod may need them to work as intended. Deleted references should always be undeleted and disabled.
Similarly to the list's discussed above in the Wrye Bash section, the rest of Skyrim's data that isn't related to levelled lists is stored in individual records. Lydia's record for example contains all information about what skills she has, what voice she uses, what she wears, even what her fighting style is and more.
ITMs are when a file has a record that is 100 percent identical to the record that its master has (usually this master is Skyrim.esm). This can happen for a number of reasons. An edit that was reversed but not deleted, a record accidentally copied, or even an error in the Creation Kit.
UDRs on the other hand are usually objects that exist in the master files, but have been deleted from the world in the modded file (or, as above, in Bethesda's own files). This sort of problem is usually less accidental and more done from lack of knowledge, or from older modding practices.
Both ITMs and UDRs have their own problems. ITMs in mods can actually reverse changes in your other mods. Say you have a mod that edits Lydia's fighting style so she now is a cowardly archer. If a mod that is lower in your load order has an ITM for Lydias record, it will accidentally be undo the changes. UDRs can have other, more serious repercussions. If a script, or another mod tries to reference an item that has been deleted, then the script, or other mod, may cease to function properly or throw off errors. This is because it is constantly searching for the missing object so it can do what it is meant to do.
ITMs are usually solved by just deleting the identical record, which removes the problem. However, some mods, including some very popular ones such as Convenient Horses, require certain ITMs to function. This is because a feature of the mod may rely on being certain that a record is properly formatted, or has the correct data in it, and therefore the mod can't risk another mod changing it. While many of these cases are marked in LOOT and therefore won't throw out a warning, many smaller mods do not submit this information to LOOT despite their ITMs being necessary. Cleaning these ITMs will break the mod. It is therefore recommended to NEVER clean ITM's from a mod unless you are 100% certain that it is safe to do so, usually if you can read the record yourself, if it is INCREDIBLY obvious (a grasses mod editing perk trees), or if someone incredibly reliable has told you it is. You should instead report ITMs to the mod author via their comments or a personal message and ask them to confirm that it is necessary, or clean the mod file themself.
UDRs are solved a different way, actually by doing what their name suggests. It instead will undelete the offending item/record and marks it as disabled. This means that in game the script or mod can still find the item, which stops the errors, but because it is disabled you will not see any effects from it in your game which prevents the errors in game from happening. Cleaning UDRs is usually safe and beneficial to your save game under most, if not all, circumstances.
While having clean mods is always preferable to having unclean mods. Knowing what is a dirty mod, and knowing what 'dirty' edits are essential (which makes that mod a clean mod) is the core thing to keep in mind.
From: http://steamcommunity.com/app/72850/discussions/0/619573787397876592/
Clean your masters = yes
Glad the guide has helped you and any other questions come up along the way we are here.
In fact, even as concerns cleaning the Masters, which has long been an almost unwriten taken for granted rule, there is a thought that it may be better NOT to - not only because the version of xEdit from Nexus WILL break certain parts of the landscape, but also - despite the fact that this was fixed in the version that must be gotten from sites other than Nexus - there is a serious question as to how the xEdit is going about their work in changing and updating it. This from Arthmoor, March 12, 2021:
"Personally my advice would be to just ignore cleaning the official master files at this stage of things. xEdit has had a number of recent bugs filed due to issues with old form versions and file data in these plugins which have caused serious errors during gameplay and have resulted in several hackish workarounds being added to xEdit to account for these things.
If a mod has been correctly made in SSE, none of the issues causes by deleted records should be a problem if you're using the CK to make the mod as should be done since the CK will not display deleted references to be edited.
SSE mods without all 5 official master files should be considered invalid because they will not have accounted for any changes those DLCs make, and you can't play SSE without them."
https://www.afkmods.com/index.php?/topic/4110-manual-cleaning-skyrim-and-skyrim-se-master-files/page/7/&tab=comments#comment-177924
I fully agree with the above and in fact have addressed certain issues regarding xEdit in another dedicated thread referenced in the LOOT Advisory Re: Cleaning Mods post linked below.
Unless the mod author or a reliable forum regular says it is safe to clean a mod, the default action is always DO NOT CLEAN.
(NOTE - It is important to note that this mostly applies to mods made using older versions of the CK or mods which have been ported - mods made using the latest version of the CK usually do not suffer from these issues, as Arthmoor referred to, above. But since there is only limited means for a person to know that information, the do not clean rule applies - as stated.)
cfs already supplied the post regarding this with a link, but I'll repost that with the other relevant link from the PINNED TOPIC Helpful Links and Reference, Section 3, Tools, Load Order, and Mod Cleaning, again:
LOOT Advisory Re: Cleaning Mods
https://steamcommunity.com/app/489830/discussions/0/1693795812306776189/
What are dirty edits and what are their consequences - a post by Nazenn
http://steamcommunity.com/app/72850/discussions/0/485622866435280490/?ctp=11#c353915309341216776
Bottom line - only clean mod when the mod author or a reliable forum regular says it is specifically says it is safe to do so. If you do not have that information, DO NOT CLEAN!