Russell, I experience this issue also. I'm using ArcGIS Server 10.3, iOS Collector v10.2.7, I have a subtype, Editor Tracking, and related tables on a feature class called "Pipes." I have no copied layers.
Everything works beautifully, until I try to sync the iPad after I have completed the disconnected work. I get the error described earlier in the thread:
An error occurred while synchronizing edits.
Unable to synchronize replica.
Replica with GUID * does not exist on the server.
What is your take on how to troubleshoot this?
Thanks!