Hm. So, you have a file directory like…
Folder
—Subfolder 1
—Subfolder 2
------Subfolder A
Your Vault targets Folder, and you have that same Vault running on multiple devices, only on some devices you want to hide Subfolder 1?
If that’s accurate, I think it’s a little dangerous. If files in Subfolder A are linking to files in Subfolder 1, when you try to access that link on a device that doesn’t have Subfolder 1, Obsidian will create a new note—and then you’ll have two notes with the same name but different content.