You can reload documents from the command line using the distribution service. See section the following section in the QlikView 10 Server Reference Manual... 25.2 Reloading a file from the command line
The syntax is "QlikViewDistributionService.exe -r=d:\myapps\document.qwv -out=d:\logfiles", but you must first configure the service to accept command line requests.
It sounds like this is just a symptom of the underlying problem. What version are you using on the server and on the development platform?
I've experienced similar problems with version 9, but it usually relates to:
Macros being executed as part of the load, which distribution denies
Connecting to a 32 bit ODBC driver, from a 64bit QlikView service (this is corrected in version 10)