If you are seeing yellow sticky notes, like the one in the image above, in PDFs that do not contain TrackChanges, the document contains "notes" – not deleted text.
To remove the notes open the document in either InCopy or InDesign (some later versions of Acrobat Professional can also remove notes) then click on the "Notes" menu and then select "Remove All Notes". (See image above.) When you save the chapter back to the server the PDFs will no longer include the yellow sticky notes. (In InDesign the "Notes" option is found under the "Type" menu.)