I have installed Foundation for Apps via bower (bower install foundation-apps).
Foundation says to use the _settings.scss for customization. However, isn't this file overwritten when I eventually have to update to the latest version (bower update foundation-apps)?
You're supposed to copy the _settings.scss file out of the bower_components directory and into your project's scss folder so that it does not get overwritten when you update. It's the only file you need to do that with.
From the Foundation for Apps Sass Documentation
The Settings File
All Foundatiion projects include a settings file, named _settings.scss. If you're using the CLI to create a Foundation for Apps project, you can find the settings file under client/assets/scss/. If you're installing the framework standalone using Bower or npm, there's a settings file included in those packages, which you can move into your own Sass files to work with.