That happens because the PDF must have changed its layout. Typically, once you add something on a PDF, it should be in the same place even if you change zoom, enlarge it, or perform any other customization.
I recommend you to open the file again and make sure to lock all the items that you have in their original position.
You can get additional info about this through the Help section available within the software. Go to Help > Contents to open the Help database, then you can use Search to look for Lock or Unlock.