rewrite_rules_array stops search working | WordPress.org

I am using rewrite_rules_array to rewrite the pages on my site. I have recently added a 2 char prefix to the site. There are a whole host of these such as shown below

function my_add_rewrite_rules( $rules ) {
	$new_rules = array();

	... quite a few rules here
	$new_rules['^([a-z]{2})/(.*)/?$'] = 'index.php?name=$matches[2]&cscountry=$matches[1]';
	... and a load more

	$new_rules = $new_rules + $rules;

	return $new_rules;
}

add_action('rewrite_rules_array','my_add_rewrite_rules');

The rewrites are all working fine and when searching the site without the prefix the pages end at the search page using /?s=term

When using a prefix e.g. https://site.com/aa/?s=term I get a 404 not found.

When debugging and checking in class-wp-query.php the query var is lost on the redirects.

Any ideas?

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