Brazilian cherry is one of the hardest woods out there, according to the Janka scale. I'm surprised you were asked to stain it--from what I remember, it's a tight, dense wood. It's harder than maple, and I know I would water-pop maple if I were going to try to stain it.
On oak, I scrape out footprints or edger marks, and then hand-sand with whatever grit screen or disc that I used for the last cut. It blends fine, even with clear water-based finishes that don't hide anything. With oil, it's a slam-dunk to blend it. Oil poly will mask any color splotchiness.
With Brazilian cherry, AND a stain, it might be tricker to get the spot scraping to blend in. I'd try scraping in a closet first, to see how well this technique is going to work. But basically, you can scrape out the footprints, and do the hand-sanding. If you water-treated it, you should do the same for the scraped areas.
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