Writing custom CSS to a theme in code appears to work. The setter runs, caches clear, save() reports success — and the column is never touched.

The cause

ActiveRecord::save() writes only fields recorded as changed:

$data = $this->_new ? $this->_data : $this->changed;

But Theme::set_custom_css() assigns straight into _data and never marks the field:

public function set_custom_css( string $value ) : void
{
    $value = str_replace( '</style>', '', $value );
    $this->_data['custom_css'] = $value;      // NOT $this->changed
    // ... clears an editor store key
}

The fix

Write the column directly and reproduce the side effects:

Db::i()->update( 'core_themes', array(
    'set_custom_css'  => $value,
    'set_css_updated' => time(),        // cache-buster on the served CSS URL
), array( 'set_id=?', $themeId ) );

$key = $themeId . '_theme_editor_custom_css';
unset( Store::i()->$key );

Theme::deleteCompiledTemplate( 'core', 'front', 'global', $themeId );
Theme::deleteCompiledCss( 'core', 'front', 'custom', 'custom.css', $themeId );
Store::i()->clearAll();

Two related notes

• Custom CSS lives in core_themes.set_custom_css, not in core_theme_css — that table holds application stylesheets.
• It is served inside a <style id="themeCustomCSS"> block and is minified, so comments are stripped. Searching the served page for a marker comment will not find it; search for a selector instead.

Related: Custom CSS that works in both colour schemes, and the var() name trap, Theme hook types are an enum of four, there is no "replace", and how to change the page title anyway