If you have a blank day on the itinerary, the PDF will not be able to generate anything for it, therefore leaving the day out of the PDF itinerary. To change this, you can simply go into your itinerary and press "Add Events" and make the day live.

Tip: You can also change the day title to explain why the day is empty as well. For example, you could name the day "At Sea" or "Travel Day"