There are only a few instances in which I can see a loss of Affiliation affecting PrC abilities.
If the organization is religious, and the PrC abilities are drawn from another source, then loss of affiliation could be akin to a cleric or paladin losing their powers (spells, SUs, etc) due to loss of support from their patron deity or a Druid's loss of powers due to becoming non-Neutral or teaching another the Druidic language.
If the organization is governmental and the PrC bequests some rights / "powers" of a governmental nature, I can see loss of affiliation score resulting in the loss of those PrC abilities that are derived directly from the governmental source (extra income, followers, titles, contacts, information source, etc). The issue here, however, is that I cannot recall a single PrC off hand that works in this manner. Furthermore, the bonuses stated (income, items, titles, followers) are directly stated as Affiliation benefits - which would of course be lost if the affiliation score fell, regardless of whether or not a PrC class was had to be lost.