There is a cipher or cryptex under the upper and lower playing areas. Similar devices were used in the movie, The Da Vinci Code, and are a creation of the author of the book the movie was based on, Dan Brown (which may be why the instructions use the more generic term "cipher" instead of "cryptex"). There are characters on rotating disks similar to a combination lock for bicycles. If the proper combination is spelled out, the cryptex opens.
In Da Vinci Pinball, the cryptex lights up a number of characters on the table that the ball must roll over. When the ball rolls over all of the characters, the mission is completed. Some of the characters are in the drain below the flippers, so the only way to get those symbols is with the ball on the way off the table. The only way to survive that is to be in multiball so that you can sacrifice a ball, or if it is the last symbol and you sacrifice your ball, finishing the mission.
If there is a light below the right flipper, the easiest way to turn that light off is let the ball slide down the left slot and down the left flipper, leaving the right flipper up. The momentum of the ball will carry it partly up the right side to turn off the light, but of course you lose the ball. If the last ball falls before the cryptex mission is complete, the next ball starts with a different set of symbols, and you won't have multiball to help you this time. Therefore it is very important to quickly identify the lights under the flippers and knock them out with extra balls you may have in play.
A way to get to a light below the flippers without losing the ball is by shaking. The accelerometers in the iPod detect the shaking and apply it to the pinball table. So as the ball rolls, shaking at just the right moment with one of the flippers in the up position may allow the ball to pop up and back out. If you use this technique, you will want to save the light under the flipper for last. That way if you do lose the ball in the process, you will at least complete the mission.
In the final cryptex mission, if you lose the ball turning off the last light of the first cryptex, the next ball will pick up at the beginning of the second cryptex. So make sure you barely hit the ball so it will come down to the main playing area and hit the multiball targets before the 10-second expiration.