In a typical workflow, you might start in Lightroom with a raw photo, then send a copy with Lightroom adjustments (Photo > Edit In > Edit in Photoshop) for additional editing. This copy will become either a PSD or TIF file based on your Lightroom preferences (Preferences > External Editing). Both file types support all the things you’d want to do in Photoshop, with the most common being using multiple layers, so either choice is fine (though multiple layer TIFs tend to be larger).
In Photoshop, once you use the File > Save menu command this new copy is saved to the same folder as the source photo, and the copy is automatically added to your Lightroom catalog. When work is done in Photoshop, save and close the file, then return to Lightroom. The edited copy should be located right next to the original (set your View > Sort, to Filename or Capture Time if it isn’t). That’s all great, and not usually a source of questions.
However, now that you have a layered PSD or TIFF in Lightroom, and if you want to continue to edit that copy in Photoshop, AND you also want to keep the layers from being flattened then you need to pay attention to your choices. This is a common source of questions.
You see, when you start with a raw photo and use the command to send to Photoshop, the copy is automatically created, and you won’t get any choice about editing the original or editing a copy. It just opens in Photoshop.
If you select a non-raw photo (JPG, TIF, PSD) you will be prompted to choose either Edit a copy with Lightroom Adjustments, Edit Original, or Edit a Copy from the Edit Photo dialog box. The choice you make will determine if the photo opens with or without layers.
If you choose Edit a copy with Lightroom Adjustments, then a new copy is created, and this copy will be flattened. This is because Lightroom can only apply its adjustments to a flattened file. You’d only choose this option if you wanted to apply new Lightroom edits that you made to the layered version and now wanted to edit this new version in Photoshop.
To open the layered version you were previously working on, choose Edit Original and it will open just as if you had used the File > Open menu in Photoshop. If you want to duplicate the layered file and open the duplicate in Photoshop, choose Edit a Copy.
To sum up, if you want to open the layered version of the photo in Photoshop, choose Edit Original.