I got the same error at some point- my issue was I was exporting the data to an FGB, then loading to SQLExpress on my Amazon instance, and using "register existing data" in the replication process from our onsite SDE. In addition, some of the FC from my feature datasets were added to the replicas without having the GlobalIDs. I was sure that had the ID's, but apparently I didnt.
One of the layers in the featureset is our parcel layer which has about 600,000+ records and I have no issue so far with time outs, but we are running our Amazon Instance in Amazon's VPC.