That's worth a blog post on InDesignSecrets.com (if you aren't doing that already).
Would using the highlight tool in Acrobat, and then flattening the page have worked?
How do you flatten a PDF with highlights?
But those points should put the fear of God in anyone who thinks “nothing bad will happen” if they edit a PDF in Illustrator.
Are you sure the exclamation points weren't introduced in the trip from InDesign-to-Snippet-to-TextWrangler-to-PrintSelection as PDF (via OSX)? I'm not suggesting that editing PDFs in Illustrator is a good idea, but you do have a complex export and edit sequence before you even get to Illustrator.
Can you reproduce the problem?
I’ve done the ID > Snippet > Wrangler route hundreds of times and never have had the exclamation points. And I’ve got plenty of screen shots to prove it.
I also have Wrangler > PDFs that don’t have the exclamation points.
The only place I’ve seen them is in the AI file.
I thought I had reproduced it this afternoon, but now, 4 hours later, I’m unable to reproduce it.
With all due respect, but I just tried it out, and the Highlight annotation did flatten properly using flattenPages() :
Or am I missing something?
You flatten highlight annotations like this:
1. Open document in Acrobat
2. Open Console (Cmd-J / Ctrl-J)
And that would do it.