This thread is a bit old, but I recently had a call with Esri support to find an alternative to replication when using branch versioned datasets. We have not implemented their suggestion yet, but I want to share their "solution" with other.
Collaborations should be used to "replicate" the data to either other internal enterprises (prod to stage, for example) or to partner's enterprises. In a distributed collaboration, the services should be shared as copies, not references. The copying via the collab should be scheduled on a regular basis and can be paused at any time. Sync must be enabled on the service.
Hope this helps someone. I don't love the answer, but we will be attempting it soon. If anyone else gives this a go, I'd be interested to hear your thoughts.