Same happened to me, until I went to the Dashboard and there was a big welcome post and migration link that restored my download files. I have to update the shortcode in my download directory page(s) but at least that works now.
Try going to your WP admin dashboard and see if you see that Welcome with info page? It included a link to restore the old version, as well.
I did lose a LOT of site stuff, however. My text widgets in various pages have completely been wiped out. Am trying to restore from backup. Not sure if related, but this was the only update today besides WordPress to 4.0.1