Is there any way to set line item status in an order?
You can try using Commerce Delivery module... It supports line items delivery status..

Project page says


  Provides basic functionalities and admin pages to handle deliveries.
  
  Each delivery need to be associated to an order. Each order can have
  zero, one or multiple deliveries.
  
  A delivery is automatically created on order save if it contains at
  least one shippable item. Further deliveries can be manually added
  from the deliveries tab under the orders menu. On the same page each
  order line item can be moved from one delivery to the other.