The cRIO-9047 (and the rest of the 904x family) all run Linux RT. There's an scp utility in Linux you could use. It's all through the console. It's pretty well documented online (e.g. here and here). It has commands for pull and push actions. Additionally, you can run console commands from LabVIEW Real-Time using the System Exec VI.
Andrew T. "His job is to shed light, and not to master" - Robert Hunter