Uploaded Images Not Showing Media Library

Hello everyone,

A social icons pack was uploaded several years ago. These images have been working fine for years, until recently, users reported our social page being void of links. The images in question were the links to our various social media sites for our different programs.

Noticeable Symptoms
The images are missing
The files can be found an browsed via FTP
The images are blank in Media Library
The image placeholders are even missing when enabled in browsers to show placeholders.

Troubleshooting Steps
Deleted all the images from Media Library
Uploaded images again from Media Library
Uploaded a different image with the same file name and it inherits the same symptoms.
Removed all Plugins
Ran website with default Themes
Occurring with WP versions 3.8.2 – 4.1

Extra Notes
These images are soft and hard coded in many places on the site, so I would rather not simply replace them with new file names, and then manually change all the references of them on the site. What if I want to update the look of the images again the future? Shouldn’t I be able to replace the file and the image would be replaced?
These file names seem to be broken somewhere, however when I delete from Media Library, the images are indeed removed, and I also see all references of the images from mySQL removed also.
Is there some sort of caching in place somewhere that would black list these file names?

Any suggestions would be deeply appreciated.