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The slightest "edit" inside the PDF (no matter if it's one punctation edit or changing the color of a headline) destroys the compliant TAGS, creating empty tags and leaving content without tags (which had perfect tags prior to the edit). We have done testing for this on cross-platforms with the same result (PC and Mac). We have tested before and after adding the required extra metadata. Same result. We have tested this with PDFs that originate from Word as well as those that come from InDesign. Same result. We believe that this is a software issue, a bug within Adobe's Acrobat DC Pro software.
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In the process promoted by Adobe you should edit your documents with InDesign or Word and re-generate a new PDF each time (which is not necessarily longer, but it all depends on the context).
Otherwise I agree with you: it looks like a pretty big bug in Acrobat Pro!
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There are times when I don't own or have the source file. I'm given the PDF and required to make it compliant AND pass the editor's "plain language" test (especially when it comes to punctuation).
I'm all for having a perfect source file. But when I don't have the source file and need to make a minor edit inside the PDF, I need Adobe to FIX the "Edit" function from completely ruining perfect tags.
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Yeah it's a trainwreck. Best advice I can give is don't do it. Otherwise you have a big mess on your hands. It can be fixed via a manual cleanup but it's going to be time consuming and labor intensive. If you can go back to the author and have them make the edits to the source file and make a new PDF, that's your best approach.
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See this related topic: https://community.adobe.com/t5/acrobat/tagged-content-removed-after-fonts-changed/td-p/11803186