It seems to me that in order for a Questionnaire to update an existing resource using definition-based extraction, the hidden id fields must have item.definition set to the URI for the ElementDefinition of the resource's id field, e.g. (for an Observation) http://hl7.org/fhir/StructureDefinition/Observation#Observation.id. If that it the case, it should be stated as a requirement, to avoid possible other (and incompatible) solutions being developed.