The term "affiliate" simply means that a trunked system radio (subscriber) is parked on a particular talkgroup at a particular site (for multi-site systems). The system is aware of what every single subscriber is doing at any given time, and so as soon as an affiliation takes place, the talkgroup is deemed "active" and channel resources will be available. You can setup this type of patch so that it's receive-only on the trunked side, so that a subscriber can park on the talkgroup to monitor.
I don't know exactly how DoITT setup these patches, so I can't speak to specifics. If they are using a console patch between a VHF resource and the trunked system, then that doesn't count as an "affiliation", and so no audio will be passed to the trunked system. Either a subscriber would need to affiliate to make the talkgroup "live", or DoITT would need to setup the talkgroup to be active with or without any affiliations.
And of course the simplest answer could be that they simply knocked the patch/link down, and it's not a full time thing.
Barring getting an official answer from DoITT (unlikely), one could also run Unitrunker on the site/cell in question and check for subscriber affiliations with these talkgroups. That would paint a clearer picture of what is going on.