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when flattened to .jpg and shows only one layer of many, e.g. a face nothing else.
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Before you flatten it, add a white layer beneath all the others.
Photoshop may be turning your transparent pixels to black because JPG does not support transparency.
Otherwise, try saving to PNG instead.
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Didn't get alerted to this notification, just seeing it now but I can sure use this info! Thanks so much .png files it is!