It’s stored in the main site options table, under the “site_admins” key.
Edit: As pointed out in the comments, the “site options” table in multisite is actually named PREFIX_sitemeta, like “wp_sitemeta”. It’s referred to as a site option internally, like get_site_option('site_admins')
.
To adjust this without editing the database content directly, you could do this:
$capes = get_site_option('site_admins');
// $capes is an array of the super admin usernames, adjust it as needed
// then save it back like so:
set_site_option('site_admins', $capes);
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