When streams split, they are considered non-dentritic or deranged. In the Arc Hydro environment, there is a way to deal with deranged terrain. Look in the toolbox for Arc Hydro Tools.tbx > Terrain Preprocessing Workflows > Basic Deranged Terrain Processing. This will show you the process for dealing with deranged flows. I have not yet had to deal with this, but the tools and possibly the online help should lead you through it.
