A standard interactive PDF contains multiple distinct layers. The background content stream holds static text and vector artwork, while an interactive overlay (the AcroForm catalog and Annots arrays) manages dynamic form inputs, digital signature boxes, and sticky notes.
When you flatten a PDF, those interactive form widgets and annotation layers are converted into permanent page contents. Once flattened, the form values can no longer be edited, wiped, or modified by any standard PDF viewer, ensuring that the visual state of the document remains locked forever.