The only thing they might do is cross reference with a general note pad entry into both PNR's. This is rarely of use though as unless an agent reads the whole PNR for notes it is often missed. Also some are reluctant to do this depending on who you get but the entry itself into the PNR is possible. It holds no weight though during IRROPS. It is just a comment to show you are taking another flight. Again unless the agent takes the time to read the notes it can be useless.