Good evening!
I'm following instructions on the guide with a fresh Skyrim SE install with the AE DLC newly purchased, and I've found that when I clean the vanilla masters as instructed, no backup is autosaved.
For reference, the specific spot in question is here:
What should I do next? I've gone back through all steps before this point a second time.
I posted it here in case it's a part of the guide that you feel should be changed - in trying to ask about this on some discord servers, various persons implied this section might not be required anymore.