We have a project web installer that installs, upgrades etc. properly. The only issue is that on upgrade we have a problem with a virtual directory created inside the application manually via the IIS manager. We have some statically linked files which can be installed in different ways, if using a cluster it makes more sense to throw them on a network file share/DFS rather than copy them individually (they are very large).
Is there a way that I can have the Wix Web project installer not remove manually created virtual directories inside our application on an upgrade? Or at least detect them and preserve them?