Indeed.

Ground staff don't look at "notes" in people's PNRs - nobody does, in fact, unless they are given a reason to go looking.

It is a surprisingly common belief here that sectors can be connected, or travel made more seamless, by "putting a note in the PNR" - some people seem to think that separate tickets can even be joined together in this way.

OP - although it appears that the second agent made you happy, what you were looking for was rather pointless. Self-connecting in this manner is always risky - and ringing up like this to "mark" the PNR in no way make the risk any smaller. (Next time - consider changing the original booking to add the new destination).