Whoo.. that's a lot of work. I reinstalled everything using TES4Files to pull the files out of the Data folder, then deleted everything that was left and replaced all my files (I had to re-add a bunch of texture replacers too, but that's okay). It's amazing how many missing files some mods had.
This might be a dumb question, but if TES4Files pulls all the files associated with a mod and there are still some left behind, those are extraneous and can be deleted, right?
Also, I encountered something odd... a couple times I found that all the files had been removed from a folder, but the empty folder was still there. ??? (I'd put a "confused" smiley here, but I can't find one.)
TES4Files simply won't work doing that if the mod is a "replacer type" which makes what is normally buried
in one of the stock game BSA files an external reference (a file in the /Data area). The principle of TES4Files
is that it is working with respect to a "mod" ESP or ESM file which references what it uses.
Therefore I recommend if you want to clean your Ob area using TES4Files, I suggest you package all the mods
that are not replacers (like better bodies, hair, or terrain textures) then take a hard look at what's left to try to
identify what replacer mods you have had installed, and make a list.
Uninstall Ob, rename the Oblivion directory (containing the remnants left behind, like replacer stuff) to "Oblivion.save"
or somthing, reinstall Ob (and SI if you have it), download the replacers (better bodies, hair, terrain, or whatever
was on your list) and install them. BEFORE you put any mods in, select all the subdirectories in your /Data
area and make an archive of them (name it "starting-setup.zip" or something). This means whatever happens,
you can restore your subdirectories to a fresh start (with all your non-esp/esm based stuff like replacers and
Darnified UI and whatnot).
Then put your mods back in and give it a shot.
As far as the left behind subdirectory, you may have a hidden system file there such
as a "thumbs.db" that Windows makes automatically when you visit the directory.
I think the next rev. of TES4Files will probably check for this as the only remaining
file and get rid of it, since the "thumbs.db" files should not stop TES4Files from
cleaning up and removing a (basically) empty subdirectory.