Comment by joemi

I think separate vaults being in different window is probably intentional behavior to clearly show that they're separate vaults, not something that needs to be fixed.

If you want to sync only some of the things from a single vault and not other things, can't you just use different top-level folders? Have a "to-sync" folder and a "do-not-sync" folder, and only sync the to-sync one. I'm not sure if that's possible using Obsidian's paid sync, but it should be possible with other sync options.