I have come across this twice, so I figured I’d post it to prevent others from banging heads into walls or other hard objects.
After running SharePoint 2010 for a few days where everything seems normal, all of a sudden I was unable to delete Service Applications and Proxies, as well as Web Applications. Also, the Configuration Wizard was no longer present. I will not pretend I know the cause of this, but I did find a way around it – and it’s as simple as writing custom scripts thousands of lines long – NOT! Simply rerun the SharePoint 2010 Products Configuration Wizard, and choose not to remove the server from the farm, and not to change settings in regards to Central Administration on the SharePoint Server (if Central Administration is hosted on that server in the first place 🙂