Must all items in the Output folder be uploaded to the server?
In your project output folder there is a folder "web" whose contents you can load it all on the server. Advanced users can also omit some data, which is only needed to use the FlipBook locally or to boot from media (CD / DVD). The following files are dispensable when uploading:
FlipViewerXpress.exe (FlipBook main path)
FlipViewerXpress (FlipBook main path)
autorun.inf (FlipBook main path)
embed (folder - if an embedded viewer version was created but should not be used)