If the files are data sources for QlikView, and they are not zipped or archived in any other way, you can load them straight into a QVW. The LOAD script statement supports file transfers via FTP, with usernames and passwords and all.
You could create a headless QlikView data transfer document that is controlled by QDS and stores the data directly into QVD files. May save you a few steps and a lot of possible points of failure.
