PDF version of the Form is not showing correctly

I have a Google Drive integration that adds the PDF version into a Google Drive folder. That PDF is missing most of the questions. When I go into the PDF editor and try to adjust things, there are many boxes that only show if I hover them. If I go to delete them, it warns me that doing so would delete them from the web form as well. 

I think what you've edited is the PDF Form. You have to edit the PDF Document. What you are getting in your Google Drive is the PDF Document. They are 2 different things.

The easiest way to fix this is to recreate the PDF Document. Delete the existing PDF Document and create a new one like in the above image.

That worked thank you EltonCris! I did not know the PDF document and form were different. Thanks.