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I've created PDF files with Photoshop, then combined them to create a 16 page PDF. Photoshop's colour profile is set to SWOP (Newsprint), with Total Ink Limit set to 235%.

Depending on how I save the file (specifically with layers or not) seems to affect both the colour and the file size. Do layers have any effect on preflighting? Specifically, I'm trying to convert the file to X/1-a format.

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The x/1-a standard doesn't allow for transparencies. So, in order to get a PDF to pass that preflight check, you should flatten your file (SAVE A COPY WITH LAYERS FIRST!). Then you could try remaking the PDF. Also, is the photoshop file you are trying to save RGB or CMYK? Make sure it's a CMYK document before trying to output the PDF to a print standard and you may get better results.

I would probably handle this a little differently though. If you have access to InDesign you can place the layered .psd files into a document and make a PDF with the x/1-a standard and it should be fine. InDesign will handle the transparency flattening for you and you should end up with a smaller PDF to boot! This method of placing your photoshop work into a document will also work with illustrator.

That said, there is probably a way to do all this right from Photoshop, I've just never output any file I've sent to a printer as a PDF from Photoshop. I'll be interested in seeing if someone has a different method for outputting a file directly from Photoshop to print PDF.

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Yes, the file is in CMYK. –  Captain Phoenix Jun 11 at 13:28
    
Try flattening the document. It's most likely the transparencies that are causing issue. –  GoofyMonkey Jun 11 at 13:45
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Turns out that the website I was loading the file too, which was checking the x/1-a standard, was at fault. This was still really helpful, thanks! –  Captain Phoenix Jun 16 at 10:35
    
Been there! This highlights a problem with auto preflighting. –  GoofyMonkey Jun 16 at 17:27

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