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I have been adding colour to a black and white photo using hue and saturation layers. I would change the whole layer, invert, and paint in what I wanted. The layers have stopped changing the whole picture and now will only affect my subjects face. I have my layers very organized, attached to each other and in different folders so I do not know why this is happening, especially since I have been changing the layers this way for hours without issue. I even took the skin layers and flattened the photo, exited photoshop, and re uploaded the new picture, but it still won't work. Is there any way to change settings or something to make the layer affect the whole picture again?
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You need to post a screenshot of your layers panel.
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Possible reasons could be Clipping Masks, Masked Groups, Knockout Layers, … so as edgrimley said you should provide a meaningful screenshot to enable us to give more pertinent advice.