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!