Hi Venu - I havn't tested it but just a thought.
As per the documentation -
The duplicate count is maintained for every file(with name, size and last modified combination)
What I observed is if the same file received second time from FTP server and File date and time is current file created date and time in FTP server.
So if the files are being created on the FTP server with current timestamp then they are always unique files right?
May be you can test it like this - Keep one file and run the channel in test mode and see if still that processes the files.