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So today, i've changed the water for my turtle , and plus i used a soft tooth brush to clean of some scum off his shell . When i put him back in the water, a few hours later, his top scutes started to come off, and there's a weird blackish brown showing on the spot the scute was (before it fell off) . I've never seen this happen before . And it's one of the scutes on the top of his shell . Also for the past 2 weeks or so, he's been shedding this clean dead skin looking flakes all over, and it's quite a bit .

What's happening ? Is he in pain ?

Can you post a picture? Any soft or rough areas? The shell usually gets darker as they get older, so this is probably normal.