使用->toBase()方法可解决,这个问题将在5.8版本中修复

 Comment::where([
     'author_id' => $customer_id,
     'scenes'    => 'article'
])
     ->join('xb_article', function ($join) {
        $join->on('xb_comment.scenes_id', '=', 'xb_article.id')
        ->whereNotNull('xb_article.deleted_at');
     })
     ->toBase()
     ->delete();

参考链接:https://github.com/laravel/framework/issues/13909