Whenever I try to render my comp from after effects, this screen appears making it seem as if I am missing a file in my original project, but I'm not. I've reloaded the footage and it has not done anything. I'm quite stuck at this point and hoping for someone to help.
As a work around, try exporting the After Effects Composition via the Render Queue using Best Settings, Lossless. The file will be very large. Then add the resulting movie file to Adobe Media Encoder. Assuming that works, you can delete the Best Settings Lossless movie file.