There is new documentation available which talks about some best practices when using the compress command while also employing geodatabase replication. Compress is a process run periodically by an ArcSDE administrator to reduce the size of the geodatabase and improve performance. Replicas in the ArcSDE geodatabase can affect the compress process. This paper describes best practices for achieving an effective compress when there are replicas.
It is recommended that you first have an intermediate understanding of ArcSDE, versioning and replication before reading the paper.
To have a look at the paper, click HERE