When you create install set you have an option to select which online server to use. Pick (check) only one that is right (works for you). You may also edit SDMCFG.INI on the system you create install set, to have only valid references, PRIOR to creating install set.
Servers are listed under the SERVERS section on the SYSTEM tab of the Endpoint Encryption manager. Each one may have a unique key to be used by the clients in communicating with the server, so I'd definately ping support before you delete any from there. Someone might have mistakenly created a few and they ended in the INIs.
If you pull the wrong ones from the SDMCFG.INI you should only see the one left when you create your client from the console. Make a backup of the INI first.