Advanced Indesign Help - PDF exporting template pages instead of page I replaced them with

I work as a freelance graphic designer and I thought my InDesign skills were pretty good, but I just got a new client who provided me with a template to use for an ebook and I am having an issue just exporting to a PDF.

Let me backup to explain the issue a little better. I was given an already completed ebook file, created in InDesign, as well as a new "template" for InDesign that is in the client's new branding style. It includes about 7 differnet pages showing layouts for different types of pages. I decided to just copy the template file and create the new version of the ebook within the template since it already has all the brand color swatches, paragraph and character styles set up. It has some parent pages set up, all very involved. I completed the whole revision and just needed to export the file to send to the client for any changes, but when I save as a PDF it only exports the orginal  7 "template" pages (that I actually deleted in the new file) and none of the pages I actually created. Can anyone tell me what is happening and how I can export the pages I need? Thank you so much!