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Three years ago I did a admin plugin that give developer or admins a quick way to delete properties that no longer are defined in code. I still use it in all my projects but it's still happens that some missing properties slip away, especially when you work in teams with several developers hacking away. Old blog post with link to code here..
I wanted this to be handled automatically so I have created an initializationmodule to do just that. It has a check if it should check for properties or no,t so you can easily change it to whatever fits your situation.
As usual you can get the code over at Gist.