Your post is not clear to understand the issue. You mean to say in all billing documents, price of second line item becomes zero or in a particular document? What is the item category of the first line item and second line item in the billing document?
Also, go to VF02 and condition tab where click on Analysis button so that you will find one more screen. Share the details here what data system is popping up there. You can also ask your ABAP team to find out the root cause as to why the value becomes zero for second line item after saving.
G. Lakshmipathi