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In this case, you'd be naming the new mod "Cleaned Masters" or similar, and then sticking it at the top of your load order. Or at least, I assume you were using TES5Edit for cleaning?
I was, yes. I didn't notice the overwrite issue until I was about to run skse to test it out. I also see a backup folder in that override list as well.
From now on, should I be cleaning one mod at a time, and then creating a seperate mod for each overrite down the road, or should I just install all the mods first, clean all at once, and make one folder for all the overrites?
Essentially, could I just create a mod for any overwrites that come up? For Example, if one file said "Better Vampires", I just create a mod for "Better Vampires", stick to the top of the load order, etc.?
That's if I were to clean mods, though. My general rule of thumb is "don't" - doing your masters is essential, but dirty edits within certain mods are required. If research (that is, actually checking author notes and mod discussion pages) indicates that a given mod really needs to be cleaned, then I'm rather more inclined to avoid using that mod in the first place. "Necessary" cleaning should be handled by their authors, and if they've failed to do that, then odds are their files will have further problems beyond those which a simple clean can fix.