I think you are loosing the connection to the server where the files are. Does it also happen when you package the file before exporting and export from the packaged file?
If yes, does it happen if you move the package to your local computer and export from there?
If no, then you should focus on your network connection to find the problem.
In order to test out your theory, I packaged a copy of the publication with all links to the User desktop and exported from there. No change in result. I should also clarify that when generating PDFs, the problems occur in the exact same ads (a publication is comprised of multiple ads, each being an InDesign file or a PDF) each time. If the network was randomly losing it's connection, I would expect InDesign to choke and crash, or that the problem would randomly occur each time.
Deleting the above mentioned InDesign folders from (AppData/Local and AppData/Roaming) fixes the problem. I am trying to isolate which file (or files) in those sub-folders could be in play. My best theory is that some important file is corrupted whenever InDesign crashes (which happens occasionally) or some cache issue.
Please make sure, if you place PDFs in InDesign they should be exported PDF/X-4 regardless which standard you use finally.
I would also recommend not to downsample in those PDFs any images and keep them in RGB up to the end.
Flattened PDFs like PDF/X-3 or /X-1a can cause huge problems in the final output.
The source of PDFs can vary greatly because they come from Ad Agencies, Clients, and vendors. While we provide clients with Media Guidelines, many agencies and clients do not provide PDFs that adhere to them.
In this particular case, the objects that are reverting to low resolution proxies have included native .AI files and Photoshop images (though CRA's have caused their own issues).
• We use Adobe Acrobat DC to preflight and try to correct issues with PDFs.
• All images we process in-house are saved as 170-200ppi, CMYK, PSD files across the board. We do not leave any objects in RGB because we are producing PDFs for a printed product.
• Unfortunately we also have some papers that go out in the PDF/X-1:2001 format, which is still beyond my control.