Hi Michael,
To manually remove a server from SmarterStats, open C:\Program Files (x86)\SmarterTools\SmarterStats\MRS\App_Data\Config\AppConfig.xml
Look for a file such as this:
<RemoteServer ServerID="1" ServerName="SERVERNAME" IP="127.0.0.1" ServiceKey="4AACE99B-59841C38" />
Delete this from the XML.
Find associated sites related to this deleted server, such as:
<Site ServerID="1" SiteID="76" SiteName="WEH Site" />
Delete those, and then restart the SmarterStats service.