Note to self, do not add books to Calibre until Copy is reinstalled.
I was waiting to hear back from Copy.com after the reformat since I had set up my Copy folder using shortcuts. But I wanted to work on my books so went ahead and added them. I also moved some books from my main library to my "vault" library (where I keep books not on my Sony).
Long story short, when Copy synced it readded all the files. Thankfully it not delete any of the new stuff. And thank goodness for Calibre's Check Library function. It made finding the duplicates easy.
So now <knock on wood> my PC is 100% back up and running. This has been an adventure I never want to take again
Also FYI for anyone who bought Colby Hodge's
Stargazer check your copy. The one I bought from Kobo was a formatting nightmare. Chapters four and five were missing and chapter headings appeared in the middle of paragraphs. I ended up just deleting it and Kobo gave me a refund.