I seem to recall that, for one thing, an agent can append some "interesting" observations in a PNR - from the time when we could see our PNR on some sites (most recently, ExpertFlyer).

I would also imagine AA can keep other notes in our profiles, including negative impressions and how many "Eagles" we merit, which is an indicator to AA of high value and at also may reflect some risk of being lost to the airline, in essence; the rating is strictly internal, how one is assigned such is strictly proprietary, and the new range is up to five (previously three) eagles).

As this is all proprietary, I do not know how one would get derogatory information redacted other than perhaps a snailmail to one of the higher ups at AA. You can see a list here.