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I figured it out. The problem was in the way I'm computing the descriptors because as you can see in the code above, I was trying to compute the descriptors on small part of the image and not on the image itself. So when I put the image itself instead of partOfImageScene, something like extractor.compute( img_scene, keypoints_scene, descriptors_scene ); it worked perfectly and I didn't lose any keypoints from the list I had.
