*Where is the theme’s custom CSS stored?*

The custom CSS is stored in the the site’s database, in the wp_posts
table. The custom CSS is the content of the post, with a title that’s
the theme’s slug, as a post of type “custom_css”. Subsequent updates are
stored as a revision of that post.
The custom CSS rules override the CSS supplied by the theme in its
various CSS files.

Ref: wordpress.org/support/topic/where-is-the-themes-custom-css/