When a book is published, we are obligated (and in many ways legally so) to include in the braille what is present in the print. An agency can certainly elect to omit parts of the book that do not apply to the student, but I do not believe that is up to the transcriber (unless you are also the agency!). The notes to the parent should be included where they occur in print. If they occur before the table of contents, put them in the preliminary pages. Include the print page number (if there is one).
If they are being omitted, place a note on the TN page to that effect. That way the reader knows they are there in print and can find a way to access them if needed or wanted.