With my thumb on top, and both my middle and index gripping the bottom. Could this possibly damage my playing in any way?
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As long as it doesn't hinder movement/create tension, it's preference.
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I don't know about damaging your playing... Steve Morse holds the pick like that iirc.
It will however make it harder for you to tap with your middle finger (not much, but a little), and hybrid picking wont be as easy to do either.
If that way feels most comfortable for you, you should stick with it.
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Usually, I'd say if its comfortable then your fine. Just like stated before tapping, and hybrid picking might be a little difficult, if at all. But, if you choose not to play those kinds of things then it doesnt matter

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I say take it back to just the thumb and index finger, just because you don't do the kind of tapping and hybrid picking that needs the middle finger now doesn't mean you won't in future and the sooner you make this change the easier it will be adjust to the new way of playing.
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It should be fine, pick holding should be what's comfortable for you, and allows you to play the best.
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