Yes - you are exactly right. You can also use the SMH GUI to generate a CSR, grab the file from that same directory and sign it with your CA and then replace the file cert.pem with your new cert (use the same name). Its a lot of work to provide custom certs for 100's of servers so I can see why nobody would want to do it and you are probably better off you doing the simpler method they provide (deleting the existing files and restarting the service).
Nelson