However, running this command removes the existing replication factor and search factor entries that are present in the server.conf file. According to Splunk documentation, the replication and search factor values need to be present in the server.conf file to maintain pre-migration data.
Is there something we are doing wrong? How do we maintain the original factors while adding the new attributes for multi-site?
That command shouldn't overwrite the existing replication_factor and search_factor entries! What version are you running?
(if replication_factor and search_factor are not present, the default values should still be present from the default/server.conf btw. use btool to see what the current actual configs are and what files are providing them)
We are using splunk version 6.4.0. I am aware that replication and search factor entries are present in default/server.conf too but there might be a case where our customer would have set custom replication and search factors in his local/server.conf file.