Obsidian doesn’t store any global settings—everything is per-vault. Further, the help vault doesn’t store anything whatsoever: every time you close it, it’s wiped. Your vault’s settings and the help vault’s settings are totally unrelated.
So, there’s a few uncertainties about “fixing” this:
- Should the help vault store settings? Arguably no, because it is designed to remain a “default” state so that folks can’t mess it up.
- Should the app store global settings? If so, how should you determine which setting a given vault should follow? If you have a global theme and a vault theme, which one wins, and why?
How to deal with this is not as straightforward as it might seem, unfortunately.