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New update - to 16.0.2 - Everything is set like it should be for the printer, CMYK, no missing links etc. Export as a PDF/x-3 or 4. Creates a blank document. I tried to create a pdf with a separate document with just text and objects, but still exports blank and some layers are missing.
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If this only happens with one document, try saving as IDML (File > Save As > InDesign CS4 or later [IDML]. Reopen the IDML flle to deal with possible corruption.
If more than one file, try restoring your InDesign preferences and caches:
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If Steve's suggestion doesn't help, try this link to a related Acrobat issue, (that also contains links to additional related discussions):