I was facing the same problems syncing with iPhone and Windows 11. I read a solution who is been working for two weeks without problems.
After that I realized iCloud Drive can’t handle multiples read and writes at the same time like it should, so I separate the config folder (Settings, About, Advanced), created one folder called .mobile and set the field to it.
The config folder has a lot of IOPS because it manages how the workspace is presented to you, (open tabs, views, themes, plug-ins), and when you mixed that with writing a note (which is constantly been write, mostly in every key you press, iCloud Drive can’t keep up).
And it’s a good practice separate the plug-ins too, because not every plug-in will properly work on iPhone.
In Windows a marked the Vault folder as “Always keep in the device” and then in the .mobile folder, I mark as “Free Up Space”, because I don’t need it to be synced with my computer at all.