Note that the relays.dat file is not what is used to populate the drop-down box in the ‘Edit Computer Settings’ dialog box (which instead is populated based on the values returned by the ‘Relay’ property).
For a Client leveraging manual relay selection, the value returned by the ‘Relay’ property will be based on the Client’s configuration. So, if some have upper case, and others have lowercase characters for __RelayServer1/2, that can lead to the scenario you describe above. As you note, you’ll want to ensure consistent configuration if leveraging manual selection (both via the endpoint level, as well as via custom Fixlets).
As for the Relays.dat itself, you can firstly hide relays by setting
0 on the relays in question (see https://www.ibm.com/support/knowledgecenter/SSQL82_9.5.0/com.ibm.bigfix.doc/Platform/Config/r_client_set.html for reference).
Additionally, you can control how a relay will populate in the relays.dat file via the
_BESClient_Relay_NameOverride setting (for which we have Fixlets in BES Support to help as well).