How to remove the WordPress version from some .css/.js files

You can check for the current handle before removing the version.

Here’s an example (untested):

add_filter( 'style_loader_src',  'sdt_remove_ver_css_js', 9999, 2 );
add_filter( 'script_loader_src', 'sdt_remove_ver_css_js', 9999, 2 );

function sdt_remove_ver_css_js( $src, $handle ) 
{
    $handles_with_version = [ 'style' ]; // <-- Adjust to your needs!

    if ( strpos( $src, 'ver=" ) && ! in_array( $handle, $handles_with_version, true ) )
        $src = remove_query_arg( "ver', $src );

    return $src;
}