How comments are stored, and what removal reaches

One comment, several objects

What looks like a single comment in a PDF viewer is often a few annotations working together. A highlight with a note on it is a Highlight annotation that holds the comment text, plus a Popup annotation, which is only the small window that displays that text. When people reply to each other in Adobe Acrobat or a similar app, each reply is normally stored as its own sticky-note annotation (listed here as "Text") that points back to the one it answers.

Removal works by type, so this structure has two practical effects:

• Ticking "Popup / Comment" while keeping "Highlight" removes the windows but not the words. The comment text stays attached to each highlight, and many viewers still list it in their comments panel. To get rid of the text, remove the highlight itself.
• Removing highlights while keeping "Text" can leave the replies behind. To clear a whole discussion, keep both the parent's type and "Text" ticked.

Page ranges and form fields

The numbers next to each type are counts for the whole document. If you then type a page range, fewer annotations may be removed than the list suggests, and the results screen tells you how many actually went.

Form fields need more thought. A field is drawn on the page by one or more widgets, and a field that appears on several pages (a client name repeated in every header, say) has one widget per page. With a page range, only the widgets on those pages are removed. The field itself, and its value, stays in the form until its last widget is gone. If every field is removed, the form is taken out of the file entirely.

Digitally signed files

The cleaned PDF is written out as a new file. If the original carries a certificate-based digital signature (the kind a viewer checks and reports in a signature panel, not a picture of a handwritten name), any change after signing makes that signature show the document as modified or invalid. Remove annotations before the file is signed, and keep the signed original as the record. Signature fields also count as form fields, so ticking "Form fields" on a signed document removes the signature field as well.

Markup that was never an annotation

Some things that look like markup are part of the page itself, and this tool can't see them. When you save a file from Edit PDF, its stamps, shapes, freehand drawings, images and signatures are drawn straight into the page content. Only its highlights, underlines, strike-outs, links and sticky-note comments are saved as annotations.

A sticky note from the editor is saved both ways: a yellow box with the text drawn on the page, so it prints as you saw it, and a comment icon in the corner. Removing "Text" takes away the icon and its comment, but the yellow box stays.

For anything drawn into the page, the clean fix is the version of the file from before it was added. Covering it with a white box in Redact PDF also works, at the cost of turning that page into an image.