Problem with cleaning vanilla masters

[somnomania]

So I'm in the middle of setting things up from scratch, redownloading everything, and I encountered a problem with xEdit and cleaning the vanilla masters. It doesn't seem to be cleaning anything; I move everything appropriately and run LOOT, and it's still reporting the hundreds of ITMs and the undeleted stuff. The log in xEdit has some stuff about things that need manual cleaning, but I don't know how to interpret it. 

I'd appreciate some help. Last time I did this I remember the cleaning part being pretty easy, but this has stymied me. At least I can keep downloading mods in the meantime.

[Greg]

This actually looks good to me. xEdit is saying Update.esm contains three deleted navigation meshes that it cannot be undeleted. I wouldn't worry about it since navigation meshes generally have to be done in Creation Kit.

I stopped cleaning the vanilla master (Update.esm, Dawnguard.esm, HearthFires.esm and Dragonborn.esm) a few years ago since these really do not have any impact on the game and it's less risky to leave these alone than to clean them. LOOT may nag about these needing to be cleaned, but these are not harmful or affect performance in any way. Mods downloaded from Nexus and other sources should be cleaned if LOOT indicates they should be cleaned.

[somnomania]

Okay, thank you. I did see a discussion elsewhere while trying to sort this out that cleaning vanilla masters was questionable at this point, I'm glad you've confirmed it for me!