The GDS systems all have PNR notes which relate to the specific PNR. Most of those notes are customer-neutral and deal with things such as noting that the passenger is traveling with another passenger booked on a ticket under a different PNR and the like.

Those same notes, however, will include references provided by front-line and supervisory phone and airport agents dealing with specific issues, some of which may be negative. Some agents will document the fact that you sought a change fee waiver and that it was denied and others will only do it if you are rude or otherwise abusive.

All of that may be collected for CRM purposes, e.g. "we gave you a one-time waiver last time" and certainly customer service gestures for various things which identify perpetual complainers.

This is not just about "naughty and nice" it is also about looking for passengers who may be targets for OPUPS on international flights, which automated systems may identify for various opportunities and the like.

All of this suggests that how you interact with others does matter. When you ask for a change fee waiver and it is denied, thank the agent for at least considering it and politely end the call.