If the CSS bundling is enabled you can try to clear the browser and nopCommerce cache.
I turned off CSS Bundling and the Custom Header CSS works. If I turn it back on, the Custom Header CSS is ignored. Wondering why, but happy to have CSS being applied to the website. :)
If the bundling is enabled when you edit the Custom Head Styles nopCommerce is generating a new CSS bundle but the name of the file is the same. This file is cached by the browser and this is the reason you don't see the new styles.