The update is currently made from Mongos in updateReplicaSetOnConfigServer(). This is just best effort.

This probably has to be done from _doReplSetReconfig however it requires some effort. I see that the reconfig is still supported when the node is not a writable primary and in the case of catalog shard won't be able to do a replicated write. If we remove this logic from Mongos and have cases when it fails in mongod, it may become even worse. Perhaps kaloian.manassiev@mongodb.com has some ideas?