During your install and testing of ADFS, you may decide to re-install ADFS (in order to start with a clean sheet after initial tests and proof-of-concepts are completed).
I uninstalled ADFS and run the setup again. I added Federation Server as the server role and configured all certificates – all going smooth so far. I jumped to creating a new Federation Service. When it comes to applying my settings it came up with a warning “Existing Web site detected”. Therefore, the Web site was not reinstalled. If you are trying to redeploy the default AD FS 2.0 Web sites, see http://go.microsoft.com/fwlink/?LinkId=181110 for details.”
I went straight to IIS console to see whether earlier ADFS sites are still there – they were removed. I then browsed to the file system folder where ADFS sites were pointing to – the files were there. I deleted them, still puzzled at this point. Back to ADFS Management Console to reconfigure Federation Service but only to be greeted by the same message!
After long investigation, I found the solution: these 2 commands needed to be executed in command prompt:
C:WindowsSystem32inetsrvappcmd delete app “Default Web Site/adfs/ls”
C:WindowsSystem32inetsrvappcmd delete app “Default Web Site/adfs/card”
This fixed the problem and I was able to create the Federation Service on IIS again.