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CLEANING YOUR MASTERS
The masters refers to the five master plugins that are contained in the main game. The Skyrim.esm doesn't have to be cleaned, and it never should be.
CLEANING THE MASTERS: Before you start downloading your chosen mods, you really need to clean your master files. It's surprisingly easy.
BACKUP: Simply copy SkyrimSE.exe and SkyrimSELauncher.exe from your main Skyrim folder into your Modding Folder.
Then copy all five ESM (Skyrim.esm and four ESM that you cleaned) from Skyrim data folder into your Modding Folder.
Setup SSEEdit QuickAutoClean
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Update.esm
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Dawnguard.esm
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Dawnguard.esm manually cleaning
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Hearthfire.esm
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Dragonborn.esm
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FIRST CHECK: Once this is done, it would be wise to go into the game, and check that everything is working correctly before proceeding
Specifically, it has been reported that some people experience a CTD around Falkreath, after cleaning their master files. It's rare, and I haven't experienced it, but it would be worth checking the area after you have done so, just in case. It can be fixed by verifying your game through Steam, but this will also reset any changes you've made to your .ini settings, and require you to clean the masters again.