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.
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/