Avoiding "PDF Modification Detected" blocking dialog

Hello,
I am working on an Illustrator script opens an AI or PDF file, extracts some information, then converts it to a JPEG.  It is designed to run unattended in batch mode, and sometimes is used to process PDF files which were not created by us, but were submitted from the Internet.  The script is working properly for most documents.
However, we sometimes end up with PDF files that cause this warning dialog to pop up:
PDF Modification Detected
This document has been modified outside of Adobe Illustrator.
How do you want to proceed?
[ ] Discard changes, preserving Illustrator editing capabilities
[ ] Keep changes, reducing Illustrator editing capabilities
Cancel; OK
The dialog is blocking, and so prevents our unattended script from running until a user walks to the console and presses "OK" or "Cancel".
The script is in JavaScript, and contains this line, which I thought would prevent this sort of dialog from coming up:
app.userInteractionLevel = UserInteractionLevel.DONTDISPLAYALERTS;
Does anybody have suggestions for avoiding this dialog?  I would prefer for it to just select "OK" automatically, but even failing would be much better than blocking.
Alternatively, any suggestions for detecting documents that are likely to trigger this warning beforehand?
Thanks!
-----Scott.

It could be that this is just caused by out-of-sync timestamps on the file.
But possibly you've got a bigger problem. PDFs generated by Illustrator may in fact contain two files: a PDF and an AI. WHen you open them in Illustrator, the AI will be edited (and the PDF will be updated when saving). When opening them in other software, the PDF part will be edited (and the AI won't be updated). Illustrator realizes this and warns you.
You know your files, you'll have to find out what happened.

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