Basically same problem. All the media (a lot as we're running Royal Slider) disappeared from view in Media Library, but all exist looking in cPanel File Manger.
But, in my case on a VPS via ServInt, Inc., with all up-to-date installation items, I CAN load New Media and then set it up inside the slider and it functions.
But all links are lost to anything prior to the update to 3.8.
The linkage has all been lost in Media Library. Yes I did all the plugin tests and about 4 hours more solid work in .htaccess files and any security issues. I do understand the above, but have not yet gone to the database to reset all of the upload paths via cPanel > phpMyAdmin if that is what the hosting company did above.
Will report back on pathway reset only if it works.
I maintain only two other blogs that use uploaded media. Both are on older themes, but the /wp-admin/options-media.php file page you get when you click on Settings >> Media are different.
One blog has never been set on "Organize my uploads into month- and year-based folders" and the settings include:
Store uploads in this folder wp-content/uploads [in a text box]
Full URL path to files http://domainofsite/blog/wp-content/uploads/ [in a text box]
This would help for a one-folder file upload area for a low-volume site.