I am running a MacBook Pro, 3.1 GHz Intel Core i7 with 16GB of RAM, OS Mojave 10.14.3, Photoshop 2019 20.0.2 I would save the file, then save as a pdf to create a smaller copy name it as xxxcopy.pdf. The pdf would get flattened when I unchecked layers in the dialog box. But here's the bizarre part, when I go back to the original .PSD that I first saved before making the .PDF and open it and all the layers are flattened into "Layer 1". Bizarre. It happened twice and the 2nd time I was really careful and sure that I saved the file as a PSD before I saved as a PDF but it still merged all the layers. Something is getting confused and the pdf seems to be overwriting the already saved PSD, even though they are different file types. I have since upgraded to Photoshop 20.0.4. Standing by and hoping the upgrade fixes this.
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