So, what you are saying is if you replica from one geodatabase sde to another sde, and happen to have representations, those same database objects are not being transferred. We have been using reps for a few years, and until 10, had no issue. Issue at 10, was when a SDE was replicated to a file GDB, Reps were being dropped, this is a bug. Reps between SDE to SDE has always worked.
Or are you referring to changing the properties on 1 sde instance and hoping that throught the replica they will change, much like domains, where if a domian is changed, it is not replicated across.