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 (links, sounds, and redaction annotations) will NOT be removed when flattening annotations. Even though technically, 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.