If you have a layered PSD or TIFF in Lightroom that you want to edit in Photoshop, but you also want to keep the layers from being flattened then you need to choose “Edit Original” or “Edit a Copy” from the Edit in Photoshop dialog box.

You will see under each of those options that “Lightroom adjustments will not be visible”, which means that Lightroom adjustments can only be applied when the image is flattened.

To apply Lightroom adjustments you have to choose “Edit a Copy with Lightroom Adjustments”, which of course will result in a flattened version of the image with the adjustments applied.