You can remove many of the blank pages from your PDF file by changing the Section Openings setting through your theme options.
Go to Appearance > Theme Options from the left sidebar menu of your book's dashboard. Then, select the PDF Options tab at the top of the page. Find the Section Openings setting and change it to "Left or rigt page section openings" for print or "No blank pages" for web. Click Save Changes before exiting the page. Then, re-export your PDF file.