Issue :
While trying to upload .swf files to the server , the following cPanel message appeared :
cpanel Virus Detected; File not Uploaded! (No such file or directory)
Scanning the file with Anti-Virus said that it is clean.
Fix :
Clamav might be causing the problem.
If you have root access to the server and are sure that the files are clean then do the following :
WHM > cPanel > Mange Plugins > uninstall clamavconnector
This should fix the issue!