I don’t understand why you need to clear anything before drawing your changes to the rendertarget. Why can’t you just draw over the region you want to change? This is purely 2D, right?
If you want to keep your rendered scene between frames, just draw everything to a rendertarget, and at the end of the frame copy this rendertarget to the backbuffer. If you rendertarget doesn’t need to change next frame, you just copy to the backbuffer again, otherwise you first draw over the portion you want to change, and then copy.
Am I misunderstanding something, or are you overcomplicating things?