Is it ok to chime in here? I was just looking at the document and the hyphen is a 'cross out' same as across the letters/words that are crossed out, its just that in the computer font the line is not low enough to actually go across the period mark, so its not a separate hyphen line but a line across the period then the correct punctuation after (or no punctuation since it was not needed in that one example). So you could cross out the period or comma same as you would the crossed out words etc. The blue color punctuation is just part of the blue section that was added to the original paragraph to improve flow.
It is probably too late for this document but maybe it might help somewhere else etc. Sometimes they really make it confusing!