Hi there,
One method would be to delete all the annotations that are inside the document when the document and annotations are loaded. Example in this guide here:
Another method is to pass in a list of only the annotations you want to export, via the options in the exportAnnotations API:
https://pdfjs.express/api/Core.AnnotationManager.html#:~:text=Description-,annotList,-Array.<Core
Best regards,
Kevin Kim