If you want to update just one piece of the RenderTarget, you can draw something onto the portion of the RenderTarget you want. There is a SpriteBatch overload that takes in a sourceRectangle. You can use your RenderTarget as the texture and the sourceRectangle as the region on the RenderTarget you wish to draw over.
If you want to clear the portion of the RenderTarget, you can either use Get/Set Data (not recommended) or a shader that makes all pixels in a designated region of the RenderTarget transparent.
This may also be relevant to your needs.