Switching to Windows Authentication

I have been using WWF for some time and recently decided to switch my authentication scheme to Windows Authentication.  Everything went well, but I later read the fine print at http://www.webwiz.net/web-wiz-forums/kb/s-active-directory-integration.htm - http://www.webwiz.net/web-wiz-forums/kb/windows-active-directory-integration.htm that "
Windows Authentication/Active Directory MUST be enabled from a clean install you can NOT change to this type of login at a later stage."  Am I missing something?  I realize that all of my users (internal to an Intranet site) will now have new accounts, but they will still maintain access to the historical data in the site.  Why do the instructions state that you MUST make the selection at the time of a  clean install?

Thanks!