Hi Krish - For scenario -1 You have to make use of the OS commands to delete the files on FTP server before placing the request file.
-> write some script which wil connect to the FTP server and delete the files.
-> call that script from the file adapter "using execute OS commands" option
For scenario -2 :
pick both the files(request and response) and set the processing mode to delete..
during the receiver determination, process only request files(based on filename/content)