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when flattened to .jpg and shows only one layer of many, e.g. a face nothing else.
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.
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!