>Rewriting an desktop app to a web app also forces us to rethink the structure and GUI of the app. Just porting our desktop app to a webapp just does not cut it. It just sounds the time to do a total rewrite but since clients will have both the desktop app and the web app, just rewriting module by module (department by department) seems to make more sense than trying to keep hanging onto VFP and its current structure.

Your app GUI is determined by user and business needs, should not depend on whether it runs on a desktop or a browser.
You need to "rewrite for the Web" just because of insane limitations of the current Web technologies, such as modal form limitations.
At FoxInCloud we consider that the user should not loose anything in transitioning from the desktop the the web; and we do it.