Comment boxes appearing on PDF in browser view, not appearing in actual file

Chrome comes with it's own PDF viewer. If you are displaying a PDF file with a non-Adobe viewer, you don't really know how much of the PDF specification it implements - and how good it implements that specification.

When it comes to editing PDF files, and then saving these edits, there are two different methods of how that modified file can be saved: When you just use File>Save (or Ctrl-S or Cmd-S), Acrobat will create an "incremental update". This means that the original file will remain intact, and the modified information will be added to the end of the document. When a PDF file is read, the PDF parser (that is, if it is true to the PDF specification) will always start at the end and then traverse all edits that were applied (this is very simplified). This is done so that when you change one typo in a 10,000 page document, you don't have to wait for a long time to save the file, it gets saved in a split second.

The second method is to re-write the PDF structure from scratch. You do this by selecting File>Save As. This will get rid of things that you've removed, and incorporate anything new or updated into the structure of the PDF file.

It is possible that Chrome (or any other non-Adobe PDF viewer) "sees" these annotation outlines, even though they were marked as deleted. You can try to do a "Save As" and see if you still run into the same problem. If the outlines don't show up anymore after a "Save As" operation, then the problem is with the 3rd party PDF viewer.