Even barefoot you want it gone. "Dead sole" can build up and impact, which isn't good for barefoot horses either. It can change how the horse is trimmed, which can alter the angles, and create intermittent lameness. Scraping off dead sole exposes the live sole, which needs stimulation from the ground to grow more healthy sole, bar, and frog material, which is essential for a barefoot horse.
The sole callus should not be removed. A sole callus will not be chalky and flaky. It will be hard and will not scrape out with a hoof knife.
It's just dead sole flaking off, don't worry about it. When your farrier comes on his regular appointment he will scrape it out if that is his normal trimming style. It's really no big deal. The wet footing has simply allowed it to loosen up.