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Foreword
If you use Alternate-Theme-Config, many weird problems can arise. It's highly recommended to uncomment theme's _config.yml right after you copy it as _config.[theme].yml. If not, you may meet problems below.
Customized 404 page not working
Updated on August 15, 2025: This issue is related to a specific theme and not to Alternate-Theme-Config.
The problem occurred after switching from the original Orange theme to Arch. The online 404 page wasn't mine, but the 404.html provided by Arch. My custom 404 page is located in [lang]/404/index.html. Because a multilingual site can only have one 404.html file in the public directory, to use my custom 404 page, I need to modify the build script to copy [lang]/404/index.html to public. The language you choose for the 404 page is either en or zh-CN, depending on which language you want. I'm using en here.
Below is the change of build script in package.json. You can change en to your desire language.
1 | "scripts": { |
Two about menus
Two about nav menus appear in the following configuration, which Friends nav menu is removed but maybe interpolated by theme's about nav. I suspect it is caused by some kind of theme config merge.
Solution: Even if configuration is not required, set enable: false
.

1 | # _config.oranges.yml |
Unexpected theme author's email
Again, stupid Alternate-Theme-Config causes some fields of _config.[theme].yml overwritten by theme's _config.yml.
My _config.[theme].yml doesn't include email, but theme's _config.yml does, which causes theme author's email rendered in my site.
1 | # _config.arch.yml |