When updating an existing trade agreement, while having the setup to
update order lines , system is not displaying the option to the user to
Update/Keep all prices and discounts

Replication Steps in AX 2012 R3

1. Take any not Invoiced & not Cancelled order and open header in edit mode.
2. Change related price in TA for one of items in the order.
3. Edit dates in green.
4. Update order lines window will appear
5. Tick Update Ship and receipt dates
6. Update price and discounts section (red) in the bottom will become active
7. If it would be confirmed with Update all prices would be updated.

However when it was used once for an order, there is no more "update price & discount" section for the order. Then user who do update dates, even do not notice that prices are also updated in the background.
Let me know if you need more clarification.