If your output is DVD and you put all your eggs in one sequence, yes you will probably need to render the whole thing again.
One can get creative with an app like VideoRedo and stitch just the rendered work area into the existing Mpeg file, but that is fraught with pitfalls.
I would typically create at least 3 or 4 Mpeg files from as many sequences for Encore, just for your reason. This will be easier with CS4’s batch encoding.