Copying my comment from the closed ticket, as it seems that this ticket is where the fun is at.
Having this new "feature" forced upon me without prior notice, nor a decent way to disable it without breaking other features isn't the way a browser caring for you experience should handle things.
I would really like to see an opt-in/opt-out preference setting for this particular window-sync feature.
After updating to 1.18 it has effectively reset my complete workflow with this browser, giving me unexpected behavior when closing tabs, opening them, or navigating from page to page.
See example:

In this I have 3 separate windows, with a starter homepage, a page I use to quickly navigate to my bookmarks. When working, I like to keep 1 of them open at all times so a quick browse to reddit or news outlet is never far away.
Before this update, it would navigate my 1 active tab to the page I want.
After this update, it will navigate ALL similar tabs to the page I want, this is NOT expected behavior.
Going to the discord to see if I could disable this feature, I was told that zen.window-sync.enabled would disable it. Which it did, but it also disabled so much more, namely pinned tabs and workspaces.
Asking for a better way to disable this feature, or better an opt-in/opt-out, I was met with "This would turn it into a destructive preference."
I would counter that this preference currently is already pretty destructive to begin with.
Opting-out in this case would imply going back to how it was prior to 1.18. So disable the sync, but keep pinned tabs, and workspaces enabled.
If this means that there is a possibility that you can lose tabs. Give a clear warning when you disable the feature that that is possible. It's a risk I'm very willing to take.