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I have two issues, firstly I am using InDesign 2020 (15.0) on a Mac running OS Mojave 10.14.6 and the documents and all linked files are in a FOGRA39 colour profile.
First in an InDesign layout I have two PSD files with an Illustrator file between them on three separate layers so the design is a photo where a hand goes over the logo. When output as a Pass4Press PDF/X-1a:2001 lines appear on the PDF where the top layer and middle layer overlap. I have tried flattening the file via the edit menu transparency flattening option using both high resolution and p4p_v10_CS4 flattener. Also have opened the PDF in Acrobat Pro, selected Flattener Preview within Print Production and applied but has no affect. I have had to rebuild the background image in Photoshop and import as a flat file to avoid the issue but there must be a way to output a clean file from InDesign? When output as a PDF/4:2008 there is no issue but the printer won't accept that file as their work flow only accepts PDF/X-1a:2001.
Second a I have a box with a solid black fill overlaying a photo on a separate layer. The box blend mode is set to Difference so you have part of the background texture showing through. However when I output this file as a PDF the box is sold black. Again have tried flattening the file in Acrobat Pro. Have also tried changing the box fill to solid yellow and solid cyan, still outputs as solid black although on screen you see the base layer texture show through. This issue also affects PDF/4:2008 files. When I export as a FOGRA39 CMYK JPEG the box looks as it should with texture show through.
Now I can create all the effects I am after by pre bulding the backgrounds in Photoshop or Illustrator then flatten and import but I need to do multiple adapts to different sizes and so this method is far more time consuming as need to take into account different live areas etc. There must be a way to correctly output PDF's that accurately resolve transparent layers and different blend modes?
Any ideas?
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When you place PDFs in InDesign use only PDF/X-4, never, NEVER NEVER NEVER, PDF/X-1a or PDF/X-3, regardless what the printer asks for.
Never use EPS neither as it causes the same problems as X-1a or X-3.
If the printer asks for a PDF/X-1a export it as PDF/X-1a even if the file contains PDF/X-4.
Use RGB images, but set the document output blending mode to CMYK.
The stitching lines in PDF/X-1 or X-3 are caused by transparency flattening, they do not appear with PDF/X-4. But they are only seen with low resolution devices and if antialiasing Adobe Acrobat is turned on. Therefore turn off antialiasing in Acrobat’s preferences.
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NEVER NEVER NEVER, PDF/X-1a
PDF/X-4 fails with some RGB blend Effects in both Illustrator and InDesign. Here a blue fill set to Difference over a white fill with the Transparency Blend Space set to RGB, exported to PDF/X-4 with Acrobat’s Output Preview on:
Exporting to PDF/X-1a flattens the transparency and exports the correct color:
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There must be a way to correctly output PDF's that accurately resolve transparent layers and different blend modes?
Your Difference blending problem sounds similar to the issue in this thread:
If the output will be to high res offset you can safely ignore the flattener stitching. When you use blending modes you have to consider the Transparency Blend Space—an effect like Difference changes significantly if the blend space is RGB vs. CMYK. The problem in the thread above was being caused by transparency blend space conficts—it was the PDF/X-4’s live transparency in the placed Illustrator file that was causing the problem
Can you package and share the problem page?