Total media file loss after autonomous downgrading

Last week, my website (www.markscherz.com)was running really well, with all plugins and theme (customizr) up to date. On Friday I started two posts but did not finish them.
Today (Monday), I log onto my website and discover the following issues:
customizr theme had been rolled back to an early version (1.x)
all of my media files were not working on the site, but their thumbnails were still in the library
numerous plugins had been removed because they ‘could not be found’ (jetpack, really simple Captcha, and contact form 7)

I re-updated the customizr theme, reinstalled the latest version of wordpress, and reinstalled the lost plugins. Photographs were mostly back on the site, but some were still not working properly. I tried changing the media file destination twice (was sorted by month and year – unticked the box, saved, then re-ticked it and saved). No change. At this point, all of the media files were still showing thumbnails in the media library, but couldn’t be inserted into posts.
I figured this had something to do with photon in jetpack so I turned it off to see if it was somehow stopping some files from working. The opposite turned out to be the case! All images were suddenly broken. I went to check the wp-content/uploads folder and found that all of the media files since 2012 have mysteriously vanished.

It seems that there was some kind of major error on the site that caused it to delete practically all of my media files, but I don’t. I don’t know what to do at this point other than restore a backup from two weeks ago—before I had made lots of progress ‘fixing my site’. Total disaster. Please help if you can.