So despite receiving these update error messages, even after connecting the Flashpaq to another open USB port, is the tuner updated and ready to be connected to my Jeep again?
Yes and no. Did you run the update procedure until you received the message, "Tuner is Up to Date"? If not then run the update again. If your tuner is up to date then, Yes.
It is not until you understand what you do not know that the learning process starts. ~ me
3865 SN: 1495208
3875 SN: 1499193