The hypervisor update call used by consumers and virt-who uses only the environment label to determine the proper environment for the system(s). If the user has more than one organization, and 'Library' is specified as the environment, the environment used in the call could be from any of the organizations. This implies that there is no guarantee that a virt-who call will properly update the data in Katello.
Unable to reproduce. setup: * in katello: 4 organizations and 1 content-host * on content host with 3 guests Katello::System.find(14).guestIds reports 3 guests as expected