We experienced issues similar to what you're describing which ended up being due to the replica generations being out of synch. A script I have running each night synchronizes our field SDE gdbs with our internal SDE gdbs, and it was synching them "From Geodatabase 1 to Geodatabase 2," and the generations became upset. I worked with Esri support, and though we never determined exactly why the issue occurred, synchronizing in the "Both" direction has resolved the issue.
To check the generations, right-click the parent SDE connection -> Distributed Geodatabase -> Manage Replicas -> right-click the replica in question -> Properties -> Advanced -> observe generation numbers. Repeat process for child SDE connection, and compare the numbers
I attempted to resolve the issues by importing/exporting messages, but in the end had to manually port the changes into the parent db and rebuild the replica.