你看的书真的是这么说的,是的话,错了!
sank 是整个句子的谓语!即是the mighty Vasa sank with all flags flying-in the harbour of her birth.
with all flags flying-in the harbour of her birth 才是方式状语（表示怎么沉的,带着全身飘扬的彩旗沉下去的）
还有which was intended to rule the Baltic是非限定定语从句修饰Vasa.
下面是一个独立主格结构：
The wind blowing strongly（独立主格结构）,He watches ahead with thinking.