Short answer: drop the PDF and download the cleaned copy. Every annotation goes: comments, highlights, stamps, links and form widgets. Page content is not re-rendered, so text stays selectable and the layout cannot shift.
What a comment really is
A sticky note is not part of the page; it is a separate object that points at a rectangle on the page. That is why a commented document can look clean in one viewer and cluttered in another, and why printing often drops the notes while the file still carries them. Removing the annotation array removes the pointers, and with them the notes.
Where a link goes
Hyperlinks are annotations as well. Cleaning a document before publishing it to a portal is often exactly what you want — an internal review link should not ship — but it also removes the table of contents links inside the file, so keep a copy if those matter.