Problem with Sims4 Studio Merged CC

I think to get the best answer I need to start at the beginning with this.

I turned off automatic updates on Origin because I am traveling soon and don't have time to update all the mods broken in the IL patch.

Origin somehow decides to update anyway, giving me no time to remove my mods folder.

(This could have caused problems later on?)

I just spent hours getting most of the mods updated and deleting the broken ones.

Clever me, I decide to run a batch fix because why not? Everything can be restored and happy now.

After the batch fix my cc folder is a mess. All of my merged folders have vanished, they aren't in the recycling bin either.

I go to the Sims4 Studio batch fix backup files. All my merged folders, and several un-merged folders that I hadn't realized were missing are in there. There are multiple copies of some files.

Some seem to work, but others don't.

Bottom line though;

-My merged folders are spontaneously gone

-Some batch fix backup merged folders work, but the majority don't

My question;

-How do I approach this and what could have gone wrong?

-Should I test EVERY copy in the batch fix folders, or are they all more or less broken?

-Should I un-merge the folders, will this help?

The only reason I ask this is because I have so much cc and not much time to fix the problem. Has anyone else experienced this?

Thanks for any help!