Flat Rate Promotion> Subtotal Should be Equal to or Greater than the Discount Item to Keep Shipping Cost Intact

When working with Flat Rate Promotions without a Minimum Order Amount set, the Subtotal should be equal to or greater than the Discount Item for the Shipping Cost to stay intact. 

Resolve by setting a Minimum Order Amount in your Promotion which is equal or greater than the Discount Item.

Please see images below: