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I have an application that is failing due to what's known as an incorrect structure tree in the input PDF.

Looks as if someone exported a few pages from a document and that was somehow corrupted. You'll open the PDF and page 1 says "7" even though there are only two pages in the document, total. So maybe they exported pages 7 and 8, and saved it wrong.

This is quickly fixed by redistilling, but I'm wondering if there's a solution that doesn't require redistilling the file. I can't seem to find any Global Changes or action lists...

I'd like to put this into a Pitstop Server workflow, and redistilling could add too much time to the process.

I'm using Pitstop Pro 10 and DON'T LAUGH Pistop Server 3.5

In the Action List editor look for "Remove metadata". This should already be available in PitStop Pro 10 and PitStop Server 3.5. I think you'll want the checkboxes for "Page labels" and "Structural information".
This action will remove that information completely, but since it's bad anyway that should not be a problem.