As the online Help states "The ADF continues to ship with ArcGIS 10.1 for Server as a separate setup named ArcGIS Web Applications. This exists solely for the purpose of supporting legacy applications. The setup includes ArcGIS Web Applications Manager, a legacy version of Manager that allows you to view and modify your web applications."; I assume that as long as you rebuild the map services the same as were with 10.0, and the directory in which the 10.0 web applications are not deleted on uninstall / install of 10.1, the legacy web applications will still run, right?