Having been deceived by Adobe's CCloud can and can't do, We are testing it out in projects VERY CAREFULLY.
I have a similar interest in in keeping the comments with the PDF client. Here what I have discovered so far from our own personal hands on real world work.
So here is what happens if you just upload another PDF let say Rev 2 the comments of Rev one stay with Rev 1 and Rev 2 starts new comments. That's ok for some of my proofing needs with clients. However...
In another scenario we want to keep all the comments with the PDF as it goes through design phases for this we have been using the "replace" feature of the of the Web interface on the CCloud. We are encountering some problems as we are not all on the same team. This could be the root of our issue and the complete workflow is still InDesign to PDF Proof with multiple cloud users that are not on a team. You can't add a single account user to your team without paying for a full "team" account on top of the current single account users that we already bought for the designer and client and photographer and copy writers and printers.
We felt ripped off paying for a years worth of "team" accounts and no folder sharing. The worst part was the no comment from Adobe over the issue, hence that lack of trust with Adobe's claims and lack of detailed information in a comprehensible format. We will not pay for another team account ever again. The Single user account has all the same software for less money. We have our own cloud environment as Adobe pulled the rug out from under us as we demonstrated the cloud environment to our clients they were shutting it down without any advance notice. We looked like fools to our clients and Adobe will have to put some reliable effort in proving they can be trusted.
Dmann90 aka Daniel C. Walters