I also faced this situation and decided to simply replace the floor with new material. I simply decided it is impossible not to have a significant seam where the wall to an airlock / atrium entry was removed. An altenative would be to use a different flooring material like carpeting or tile where the break occurs. It worked for me in some cases. You can even frame the hardwood floor with a contrasting wood, or planks laid perpendicular, so it looks intentional. When you get in the situation where you are piecing together a floor or removing walls, the salvage of the old floor is obviously more difficult and requires thinking outside the box. In most cases, it becomes easier to simply replace the floor.