Flattening annotations is the act of painting the annotations directly on the page to which they belong so they are not editable anymore. This will permanently write an annotation into the document. For instance, a custom signature stamp can be flattened so the signature is added to the document itself and doesn't sit on a document as an annotation anymore.
Note: The following annotations (file attachment annotations, links, sounds, and redaction annotations) will NOT be flattened when flattening annotations. Even though technically file attachment annotations, links, sounds, and redaction annotations are annotations, they contain actions that would also be removed if the annotation was flattened and so they remain to not interfere with the functions placed in the PDF.
From the menu, choose Comments > Flatten all Annotations
From the menu, choose Comments > Flatten Annotations on Current Page