I also have the same issue. It is really annoying that every time the “open another vault” button is clicked, it reset the zoom level to all the opened obsidian windows.
I am using Obsidian 0.12.5 (installer version 0.12.3), MacOS 10.15.7
Updated:
You can use Obsidian URL to open the target vault directly and this will respect the zoom setting. See here: