For example, for this patient

https://bonnie-fhir.healthit.gov/#measures/AE6C65DA-F070-4C68-8D70-6503AD4F2706/patients/60d49f6098086b41b3e5f702/edit

relevant logic snippet:
 
{{define "Qualifying Diastolic Blood Pressure Reading":
[Observation: "Blood pressure panel with all children optional"] BloodPressure
let Enc:GetEncounter(BloodPressure.encounter) where BloodPressure.status.value in {'final', 'amended'}}}
 
{{define function "GetEncounter"(ref Reference ):
singleton from ("ATR Encounters"
//AdultOutpatientEncounters."Qualifying Encounters"
x where x.id = Global."GetId"(ref.reference))}}

The logic above shows that a list of Observations are retrieved, then it tries to find the corresponding Encounter by matching the .id ; i.e., BloodPressure.encounter is a reference from the Observation to the Encounter. 

Bonnie FHIR does not allow me to set the Observation.encounter (reference) to an Encounter which has already been created (or imported).  The "Attributes" section for Observation: Diastolic blood pressure has a menu "Value Set/ Direct Reference Code" with an option for "Encounter inpatient". This will create a new Encounter instance, but this test case does not need "Encounter inpatient". It needs to be able to reference Encounter: Home Healthcare or Encounter: Emergency Department (which were already imported from Bonnie QDM patient data).  Setting Observation.encounter should not force me to create a new Encounter resource; I should be able to pick from existing Encounter instances.