I was the one who wrote that guide. I have just finished rewriting it since it was later learned that people with faster disc drives get different results. I have copied and pasted the updated steps below and hope that this solves your problem.
2.B. Clean the Update ESM
To remove errors in the Bethesda master files, STEP recommends that they be cleaned with TES5Edit. This ensures maximum stability and compatibility within the Skyrim modding experience. At this time, Update.esm will be cleaned in the following manner (the DLC should be cleaned later according to instructions on their corresponding "mod" pages):
- Make a backup of Update.esm from <skyrim>/data directory by copying it to the desktop (or somewhere else handy).
- Run TES5Edit through Mod Organizer.
- Right-click the list of plugins and choose [Select None].
- Double-click Update.esm.
- Wait for the Background Loader: finished in the right panel, and then right-click [Update.esm] and select [Apply Filter For Cleaning].
- Wait for the [Filtering done] Processed Records: message in the right panel, and then right-click [Update.esm] and select [Remove "Identical to Master" records]. If the Warning! prompt pops up, click [Yes, I'm absolutely sure].
- Wait for the [Removing "Identical to Master" records done] Processed Records: message, and then right-click [Update.esm] and select [Undelete and Disable References].
- Wait for the [Undeleting and Disabling References done] Processed Records: message, and then click the [X] at upper right of the program window to exit the program.
- At the prompt, checkmark Update.esm and Backup Plugins and click [OK].
At this point there are two possible outcomes, dependent upon how fast your disc drive is:
- In the first case (typically slower drives such as HDDs), the Update.esm is now no longer in the data directory.
- In the second case (typically faster drives such as SSDs), a cleaned Update.esm is now in the data directory (compare the filesize to your backup of Update.esm to verify that it has been cleaned--it should be smaller).
In the first case, you should now do the following:
- Restore the backed up Update.esm from step 1 to the data directory.
- In Mod Organizer, at the bottom of the left pane modlist is the Overwrite mod, now labeled red because files have been written to it. Double-click to open it.
- In Overwrite you will find two items: a TES5Edit Backups folder and Update.esm. Since you already restored your own backed up Update.esm to the data directory, right-click and delete the TES5Edit Backups folder and click Close.
- Right-click Overwrite and select Create Mod..., name it Cleaned Update ESM, and click OK.
- Drag and drop the new Cleaned Update ESM mod to the top of the left pane modlist.
In the second case, you are done! You can safely delete the backup as you shall not need it (if you wish to restore the original uncleaned Update.esm later, you can simply verify Steam cache and redownload it).