I thought it was fixed, but when I opened chrome on my work pc,
there it was again!
changed bookmarks (on bookmarks bar) appeared as new ones,
while the previous one remained!

Thank you for filing this bug.

The code for synchronizing bookmarks across multiple devices is very old and hard to maintain or extend. We are in the process of migrating this code to the latest architecture of Chrome Sync. It's possible that many existing bugs are rooted in the old infrastructure. Together with the fact that the new infrastructure will make it much easier to identify and fix bugs, we would like to finish that migration and not modify the old implementation. We expect to rollout the new architecture towards the end of the year.
We are sorry if this has been a frustrating experience for you, but we believe that our chosen approach allows us to ship a better experience sooner.

what if I try this from chrome://flags?

Enable USS for bookmarks sync
Enables the new, experimental implementation of bookmark sync – Mac, Windows, Linux, Chrome OS, Android

#enable-sync-uss-bookmarks

I've had #use-sync-sandbox disabled, 
I enabled it, is it gonna make things better?

For about 1 month I have a similar issue. All bookmarks that have no name get duplicated. There is no renaming involved. those bookmarks are rather old. When I give them a name the bookmarks are not duplicated any more. The duplication process goes so far, that there are hundreds of them.

Platform: Linux + Mac
Version: Chrome Canary

Maybe this is related if not then please add a new ticket. 

I'm running into this as well, running a Macbook Pro and Ubuntu or NixOS laptops.

Patrick, I'm going to try enabling that #enable-sync-uss-bookmarks but first I'm going tomake sure I've backed up all my bookmarks to disk. :)

I don't think #use-sync-sandbox helps, 
I disabled it again, 
anyway, I've had some issues, 
but I think it's working fine now,
maybe it needed some time and/or operations 
in order to work properly