Comparing documents and false positives

Hello,
I often have to send a proof of a book to a printer. The proof is a PDF. When they return a soft proof--another PDF that they will use to print--I need to quickly compare the two to make sure that there have been no changes in the text.
The Compare Documents feature certainly beats a side-by-side eyeball scan. But I often get a lot of false positives, words are flagged that actually have not changed.
It appears that my PDF, exported from InDesign has some hidden discretionary hyphens. In ID these are used to make sure a word breaks at the end of the line at the correct syllable. They are invisible when printed. In a PDF these are not necessary because the text ain't gonna reflow, right?
But when I compare the soft proof to the original PDF, words with discretionary hyphens are flagged. Somehow the printer has stripped the discretionary hyphens. That's fine but what must I do to get rid of them in my PDF?
Below is an example. The PDF shown is the one from the printer. The comment box shows the difference from the original PDF, though there is in fact no difference on the page.
Any advice would be appreciated.
Tom

I like Acrobat's text comparisons, which have saved me from bad goofs several times -- mostly stray key-strokes, but once I caught an InDesign footnote numbering snafu.  However, the false positives have always been annoying even without flagging every single discretionary hyphen.
I imagine you have tried the image method for comparisons, a modern version of the old trick of putting printouts of the old and new versions of a page on a light table to find differences.
I don't recall seeing comments of the type "undefined", but does re-sorting comments by type at least isolate these so you can step through the rest?  I'm no scripter, but can a javascript mark or eliminate comments containing hyphens?
More drastic, would it be worth trying to eliminate the discretionary hyphens?  For instance, you could apply Harb's "Freeze Composition" in InDesign, and then search-and-replace all discretionary hyphens.  (Read the comments on the In-Tools site, as well as those in the InDesignSecrets blog it links to because you might want to modify the way it handles hyphens.)
Good luck!
David

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