Annotations plug-in allows you to import notes and comments from PDF into a source InDesign file. For successful import of text edits and space dependent notes, both documents need to be identical. The plug-in can match different pagination of the PDF and InDesign documents, so you can export just a one page PDF for proof or import notes from a whole book PDF to a single chapter file. Annotations can also process PDFs exported as spreads.
DTP Tools recommends working from the InDesign document end to its top. Doing so will minimize misalignment of comments and notes as edits are accepted.