So, after pulling my hair out for days after getting a failure message when running the CU7 prerequisites check which told me the domain functional level needs to be 2003 native or above when it is already at 2008 R2 I have found what I think is the reason for this and need help resolving the cause.
It looks like when the organization upgraded from Exchange 2003 to 2007 the then Exchange administrator did not follow the correct process to remove the 2003 servers, he just formatted them and called it good!
This means we still have references to Exchange 2003 littered around our AD and these appear to be the reason the CU7 prerequisite check complains about 2003.
So my question is how can I remove these references from AD and clean up the mess left by my predecessors predecessor?
We still have 2007 running in co-existence with 2013 thanks to issues with a third party which uses POP3 connections and are reluctant to allow us to change the server settings in the POP3 client, open port 995 and tell it to use SSL so this co-existence is going to be around for some time unless we can force them to change things. While we have 2007 running we need to upgrade to CU7 to stop the random failovers of databases from server to server known to happen in this kind of setup and which always seem to happen at the worst possible moment.