Then you have to use the EXEC command, because it is the only way to communicate with the OS.
In the EXEC command you could write OS command. An example for windows: exec('cmd','del C:\myfile.txt')
Because you will need some commands to detect duplicated files and delete this files, I would create a batch script an execute this script from the DS with the EXEC command. I know, that this is possible, but I am not a shell expert, so I cannot tell you how.
Another way is to avoid duplicate files. I do not know, how the files will be created, but if you have a system, that exports its data, you could delete all files in the folder, before loading.