Indeed. The eleventh Doctor clearly stated that all the Dalek invasions of Earth in the RTD stories have been rewritten from time and no longer happened, explaining Amy's lack of knowledge of who the Daleks were. However it would be nonsensical to write the main timeline as though those stories never happened since from the audience and the Doctor's perspective they did. The treatment of stories where the rewriting of time happens within the narrative of the story should not be any different to a longer time-framed example like the one I've given above, otherwise the Doctor's chronology makes no sense whatsoever.