Some years ago, Rick Borstein wrote a great article about how to flatten PDF comments. Adobe doesn't officially support this script. Running the script will essentially "burn" the comments into the PDF, so they'll no longer be viewable in the comments pane, and they will be visible when the document is placed into InDesign.
At some point, Adobe removed the script from their site, but I keep seeing people ask for it on various Adobe forums. So here it is:
event.target.flattenPages();
I still use this regularly in Acrobat DC. I set it up as a custom command and added it to the Quick Tools bar. Apparently you can also do this same thing using a feature in Preflight, single fixups. But I think a one-click solution is easier.
Here are a couple of Adobe forum posts where people have been discussing this function:
Placing PDFs in InDesign
How to "flatten" a pdf in Adobe Acrobat X Pro
Tutorials specializing in long documents, print production, InDesign, Acrobat, and occasionally Knitting.
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