You can force a guide download by turning off or putting in standby the Hopper and all the attached Joeys. You also have to be sure nothing is recording or scheduled to record for the next 30 minutes or so. After a few minutes a message should appear on the screen indicating a guide download in progress with a percentage progress report.
Guide download worked great in my Hopper 3. I did procedure four times. First three times the new guide advanced a couple of hours. On the third time the download had a full nine days in the guide. I did the guide download a fourth time and no new advancement. So it appears the guide download will work every time even if the guide has the full nine days.