If I am understanding your question correctly, you cannot run the file through the server and have your Visual Discovery pages render.
Two things to check/try:
1. Is APPROOT identified as an alias to your web server? (APPROOT refers to the apps folder under IBI)
If you try to run any WebFOCUS report or web page saved in projects, and are unsuccessful, APPROOT may not be defined as an alias.
2. Are you accessing the Visual Discovery pages from a different machine?
Check your Visual Discovery HTML code to see if the local hard drive is referenced. IF so, you can't see the pages from other nachines.
I have both APPROOT identified to the Web Server and I use relative paths for the ID.
For example, an snippet from one of my Vis Dis pages which tells the HTML where to get the data from:
http://localhost:8080/approot/myapp/myvisdisdata.txt