Because there are several processes involved:
What software produced the graphics? What format are the graphics in? What color space? Exactly what settings are you using to create the PDF file? What PDF reader are you using to view the PDF file? What error messages have you received?
What's the format of the linked files?
I know that you said that all of your fonts are good but have you tried using a different copy of each font as a way of being sure of that? Also check your pdf in Acrobat to see if all fonts been embeddd. You can find this out find out through File>Save As Other>Optimized Pdf>Fonts option in the PDF Optimizer window. If not go back to InDesign and in the Advanced section of the Export Adobe pdf dialog make sure that subset fonts is set for 100%.
A friend of mine posted this question, but I am the one dealing with the issue. The files are a combination of ai and eps files, CMYK color space. I exported the pdf using the Press Quality setting. I am viewing the file in Acrobat DC. I'm using InDesign CC 2015 (because of some plugins I use that aren't licensed in ID CC 2017), but I have also used InDesign CC 2017 to see if that would fix the issue. Still the same - a different list of errors each time I export the pdf.
To answer Bill Silbert, the fonts I'm using are Times New Roman and Symbol. (I had to change the Symbol font from the version that came in some of the source files to the one on my computer.) My pdf export subset fonts is set for 100%. (I never change that.) Usually, I will get an error message or notification of some sort if I'm using fonts that can't be embedded (both in Illustrator and in InDesign when I export a file). No error messages of this nature have appeared.
I've worked on other mathematics books for this client and have never had this issue. Any other suggestions?
Can you make one of the EPSs and one of the PDFs that are troubling you available for download?
You may upload the samples to a service like Dropbox and post the download link here.
Without seeing the files its hard to help.
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My latest knowledge on PDF files is, that they are best to be PDF X/4 files. AI files may also be saved as X/4 files. Fonts do not to be outlined but should be embedded.
It could help to post a problematic file so that the specialists can look at the data.
I apologize for the delay in my response. I just exported the PDF file again using the PDF X/4 setting as suggested by Abambo and as far as I can tell, all links appear to have exported correctly. Thank you so much for the help! I will post again if I discover any errors that I didn't catch before posting this message.
If you get AI files and don't have the used fonts on your computer, don't open and save them as it will destroy the content. Simply place the AI file in InDesign.
Don't use EPS files. Try to convert them via Distiller to PDF files and use them. There may be several causes why the EPS file will not work, we cannot do enough forensic from the distance to clarify why you have this problem. But avoid EPS in modern days as much as possible.
If you ask for PDF files, require PDF/X-4.