You can use the action rules in Auto FTP Manager to remove files that do not exist on the FTP server.

While creating an automated transfer profile, specify the action rule to transfer files from FTP server to the local folder location and also check the box to delete files from a local folder location if they do not exist in the FTP location.

Once you create the transfer profile you can add a schedule to automate the file transfers. The schedule will run at the configured time. Your files will be transferred and the files which are removed from the server will also be deleted from the local folder.