Ahhh, if you mean manually changing the state_id's using a SQL update...be prepared for potential data loss. I am not sure what kind of replica's these are...if they are one way, SDE.DEFAULT parent to File Geodatabase replicas..you might be okay, but my guess is that you might corrupt your replicas.
If it were me, I would take the safe approach and "unregister" the replica's using the ArcGIS desktop tools. Once you do that, query the versions table again..you want to get it so you only have DEFAULT. Once you are there, then compress (kick everyone out of database first)..and your state_id on default should be 0. Then register your replicas again.
Also, I personally have not tried the methods outlined in the article below, but it clearly states to implement these methods at your own risk. That's your call. Also, Esri support would most likely not recommend this approach, but if you are the type of person that voids warranties, backup everything up twice
Hussein Nasser: The Unorthodox Way to Compress a Replication-Enabled Versioned GeoDatabase to State ...