We discussed this in the slack channel (#api @ https://netapppub.slack.com), but for anyone reading this thread not involved in Slack, here was the answer:
Something to check. Were these relationships created through the REST API or via some other method? If it was some other method, do they have a policy-type of async-mirror or vault? If so, they are not supported in the REST API (and won't be returned) until you upgrade to 9.7 where they are supported.