With publisher in picture you can always schedule application Source document not user document. You need to have proper folder structure.
Check this for more details.
The back end (publisher) does the
- reload of documents (.qvw)
- distribute of the reloaded documents to the server (front-end)
The front end (server) is where the user interact with the documents
So you have to schedule the .qvw2 (sourcedocument) reload on the publisher
some useful info here
and in the first pages of the attached pdf