You may have noticed that the Active Roles Admin Guide specifies, for the manual configuration of the Azure Back-Sync in the Sync Service, that replication should not be active between AR instances:
“NOTE: Before adding a replication partner in a Replication environment, make sure to perform back-synchronization in the Service that is configured with the Publisher database.”
This is a documentation defect (TF00222269). The Azure Back-Sync configuration can be safely configured (Manually or via the Wizard) without breaking the replication between AR instances.
This will be fixed on a future release of the product. Please refer to this article for updates or contact support referencing the defect ID TF00222269.