Susanta,
It may not be the easiest solution, though it may be, but I would suggest trying to model the overbanks/floodplain with a 2D Flow Area (available in RAS 5.0 Beta). If you’d like to maintain the XS data, as is, in the model (with wetted low spots, as mapped), then you might consider a simple post-process to clip the disconnected mapping. Though, if the mapping that appears disconnected is in fact active during large events, another look at the modeling approach may be warranted.
Let me know if this isn’t helpful,
David