Does the NPrinting service have permission to connect to the ftp site?
Yes you can reload the QlikView document in NPrinting.
Have you looked at the NPrinting log to see why the task failed? NPrinting creates a separate log file for each day on the NPrinting Logs folder, with separate files for desktop jobs and Service jobs.
I would start by looking at the log file, and comparing the log for running the task on the desktop which works and running on the server scheduler which doesn't work.
You can reload data in a local QVW using a reload task in NPrinting. See the following: How to Reload Data into Your QlikView Document
You'd have to look at the log files for the NP server to see activity (or lack thereof) at the time that you scheduled the task.