I have had similar problems. It’s very unclear to me how the settings sync flow is supposed to work (what overwrites what, what is tied to the device, what is tied to the remove vault, what is tied to the Obsidian account independent of any vault, what is the ultimate source of truth, etc). For me this is by far the most confusing part of Obsidian. Pretty much every time I set up a new device, it doesn’t work the way I want and I give up on tweaking it, because it’s too laborious to mess around with it and try to figure it out. I looked for a doc page about it in the help vault, but didn’t find one.