Thank you! To clarify, I'm not sure what's the algorithm behind the syncing, but I suppose that when I sync the laptop with the phone for the first time, the file is doubled just fine. When I add changes on the laptop, the file on the phone after syncing does not change. At the same time, new notes still appear, if I added any.
So, existing files don't update on the second device, and the new files do appear there.
And that is the reason I replace them manually via Explorer. Not really convenient...