We are using the flatten fields and comment java script, but it doesn't lock the comment fields. Does anyone have the code to lock all comments so we don't have to do manually?

If you were to edit a signed document it would destroy the signature. So you have to work with what is signed, not edit it.

Hmm, as described there won't be any annotations: "All annotations—including form fields, comments, and links—on the specified range of pages are flattened. They may have appearances, but they will no longer be annotations."

Do you see something different?

I'm probably missing something, but my view of "flattening" comments is to turn them into page contents so there are no longer any comments. Given that, there's nothing to lock afterwards. What JavaScript do you use?