Palette changer tools?

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Yep, since it compares the relative pixel positions, the frames should be at the same position inside the box. It's best to align the top and left with the sprite's pixels (you can use the zoom for better precision).
The one single correct sprite there results from the oridinal source frame (pink) being copied ovet to the destination frame's position (blue) after recolouring.


While it would be possible to add frame recognition, it's require a lot of work and would probably be rather slow (due to checking many pixels) aaand I don't really have the time at the moment :<