Replacing PDF files in desktop deletes comments on web colaboration

I am trying to build a colaborative workflow, and due to the licensing restrictions in previewing fonts, we are experimenting with using PDF files.

We want to use the comments features as a way to track changes and informations.  However, when I replace the file in my desktop and it Syncs, it changes the link, and loses all previous comments.

It does work when I use the replace feature in the web browser version, but that is quite a hassle.

Is there something I'm doing wrong?