I have learned and understand that once freighters are established on their routes that upgrading is pointless as far as engines are concerned; as they only move 1 grid per turn. However, before I came to this realization I created a new freighter with multiple engines. I decided to upgrade my entire trade fleet to the new freighters with a cost of 3000 bc or so to do them all. Once I agreed, the game deducted the credits and nothing happened. I did it again, and again the game took my money but gave me nothing in return. It did not even upgrade the ships. Typically you get the "1~3 weeks upgrading" text under the ship while it's upgrading.