A unique feature of PDF Annotator is the ability to see all of your saved annotations in another PDF application, and still be able to process them in PDF Annotator the next time that you open it. However, if you prefer, you can also irrevocably merge all your annotations into the document.
To irrevocably merge all your annotations in the document, select Edit Melt All Annotations.
Alternatively, by choosing Extras Settings Save Persistence instead of the default setting Always editable, the setting Editable until saving or Not editable can be substituted. Annotations will then automatically be saved, either immediately, or every time that the document is saved.