Will files from the protable recorder be cleared once they are sent to the Relay Server?

Yes.  If there are unpublished recordings on the portable recorder, the next time you open the Relay recorder from the portable device, you'll be asked if you want to view or submit all of the saved recordings.  If you view the available recordings, you can choose to submit only selected recordings, or submit them all.  Once they've been submitted to the server for publishing, they will be deleted from the portable device.