HELP!! Two separate WP-Content Folders

I logged on my site yesterday and everything failed to load. All my plugins and customization was gone, and I still don’t know why. After re-uploading everything through my FTP, I know have the old WP-Content folder as a sub-directory to the new WP-Content folder. I can’t delete the new folder. I get a Error 550, and I also can’t move the new WP-Content folder. It won’t let me. Any suggestions????
Adam