I ran a test with this scenario. I created a two-way replica from one sql server database to another. I added the child geodatabase feature class to ArcMap, added a join, updated a field based off of the join, did not remove the join, and then executed the 'Export Data Changes Message' tool from the Distributed Geodatabase toolbar.
I was able to successfully create the XML file and import this into parent geodatabase. So, the join/relate should not be affecting the replica. What is the error message you are receiving?