If you flatten before you save for web you loos your layers, your work. If you use save for web or save as to save an image file in a file format that does not support layers like Jpeg and PNG. Photoshop will temporary flatten the current document change color depth to 8bit if need be, optionally convert to sRGB color space then encode the images into the file format you want to save, write the file and then revert your document to the state it was in before you did the save for web or save as. You can then preserve you work by saving the document into a file format that supports layers, PSD, PSB or Tiff.
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