This conversation has been merged. Please reference the main conversation: Photoshop: How did I get a flattened PSD after saving PDF?
Once complete, I saved the .PSD. Afterwards, I decided to Save As a Photoshop PDF, set for Smallest File Size. Now I got my finished PDF!
But wait, I realized I needed to make a couple edits post .PDF, so I go back to Photoshop, layers are still all there :) So I make my edits and Save As a .PSD. I decided to close Photoshop before exporting another .PDF because I had other activities in line.
Upon my return of opening the original PSD... all my layers are gone now.
I have recreated this weird loss of layers twice more to verify my order of operations. This is totally lame!