I recently decommissioned an Old Exchange 2003 server. Prior to the decommissioning, the environment consisted of 2 EXCH 2010 and that one EXCH 2003 server. I went through all the steps listed in Microsoft documents and online in how to remove the server completely (pruning the AD and all that jazz). When I go to Exchange Management Console it still lists 3 total servers in the "Server Summary" column in the Organizational Health tab. When I click manage servers, it only lists the 2 EXCH 2010 servers. I am aware this is only a cosmetic issue but I would appreciate it if anyone can share some advice on how to fix the issue.
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See if `%userprofile%\AppData\Roaming\Microsoft\MMC` contains a saved settings file for the EMC - if so, try to delete/move it and open up EMC again – Mathias R. Jessen Aug 19 '14 at 17:30
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There's no saved settings file... – El Chapo Gluzman Aug 20 '14 at 13:04
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Update:
If the server is truly removed from the environment, you may just need to click the link at the bottom of the Orginization Health tab that says Last Updated: timestamp. Click here to access the latest data. If not, then my original answer still applies, but you will need to update this data after removing the server.
Original Answer:
In order to resolve this you will need to remove the Exchange 2003 server from Active Directory using ADSIEdit.
There are some helpful directions here: http://blog.dargel.at/2012/02/23/remove-legacy-exchange-server-using-adsi/

Tim
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BTW, this should have been cleaned up when Exchange 2003 was uninstalled from the server. If the uninstall did not go smoothly or was not performed, then that is most likely the cause of this. – Tim Sep 11 '14 at 12:39