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To avoid this I fold the stitched piece and the backing piece in a different order. For the stitched piece I fold the sides, top and bottom before I fold the corners. (As illustrated with with red paper) For the backing piece I fold the corners before I fold the top, bottom and sides. (As illustrated with yellow paper.)
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Then the stitched piece and the backing piece fit together nicely and the layers of fabric are more evenly distributed.
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