Hi Anthony, I've been looking into this issue with another user. If a layered file is opening as a flattened document, it's possible the layered PSD image became corrupted at some point and Photoshop is just loading the flattened composite. I suggest running a disk scan to see if there are any weird hardware issues that might be causing this.

• Using Layers In Photoshop

Also, try resetting Photoshop's preferences, just to rule out a corrupted preferences file. Could you send a copy of the PSD file (the one that became flattened) to jrubbo AT adobe DOT com?

UPDATE: Ok I thought everything was worked out but just now, My office co-worker just tried a test. She has Photoshop CS6. She opened a PSD file that she had been working on and saved it with the name TEST, as a PDF with the save options 'save as a copy' & 'layers'. Once she did that, her PSD file lost all its layers and didn't give her an option to undo or step back in the history or revert. She closed the file and reopen the original PSD, under the original name and all her layers were gone. This is not a fairytale, I watched the whole thing unfold. There’s definitely a glitch!

What I do now is simply, save my PSD file to Jpg files. Then open the Jpg files and convert to PDF.

In this quick Photoshop tutorial, we’ll learn how to export Photoshop layers to files. By using a built-in Photoshop script we can spend up our work and save quickly layers to individual files like Png, Jpeg, Psd and other file types. The export option lets you export all layers in a Photoshop file regardless if they are hidden or visible. It also gives you the option to export only the visible files. You can select which format you export the layers to. You can export each layer to individual PSD files of their own or export them as JPG, PDF, PNG, BMP, and TIFF files.

I’m not taking any more chances of losing my layers. Having the same issue – this was never a problem before I got Adobe CC. I was working in a PSD file with multiple layers, saved my.PSD file then did a 'save as' and saved a PDF with a separate file name - did not check any boxes or un-check any boxes and when I went to re-open my PSD file (that was saved BEFORE making the PDF) all layers are gone. I have been using PhotoShop and making PDFs for client-proofs, etc. For more than 10 years with no issue until Adobe CC.

OP is not crazy or doing anything wrong. I just lost more than 6 hours of work. I just don't understand why the save as a pdf action overwrites your psd file. That seems a poor design feature. I am not trying to convert my file to a pdf. I just want to save a copy so other people can see what I am designing and approve. To me its like doing something in a Word doc and then saving as a pdf to share to others and the pdf overwrites the word doc.

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I mean really, how many people actually want to overwrite their psd to a pdf? I can delete the psd later if I want, but why make us risk overwriting our work in psd? I guess this problem still exists?!? I've been saving PSD as PDFs on a project that has multiple files. Been doing this for the last few weeks when making multiple edits to the files. Then, BAM out of the blue, I lose my PSD layers on one file while saving as a PDF.

Using Layers In Photoshop

And, yes, all the proper checkboxes were on. Then I created a test PSD file and observed all the options, and all was well. Saved a PDF and my layers were there, intact. There's definitely something. Maybe my one file corrupted? Maybe those who continue to have the problem may have a hardware issue along with it? At this point, I'm weary of saving a PSD as a PDF.

Going to opt for a JPG going forward, then converting to PDF if need be.

Photoshop's PSD format saves projects by storing individual layers. When you save a PSD file for external use rather than editing, you must convert the project to either a raster graphic or a vector graphic. Raster graphics store images as pixels, so their quality drops when you enlarge them. Vector graphics store images using mathematical algorithms and they remain clear no matter how much you enlarge them. If you create graphics for large-scale use, such as a banner or a billboard, convert them a vector graphics format such as PDF.