Transmission problems

OK, Jeep went to dealer service and their diagnostic flagged up 3 transmission faults. I actually went in for a thermostat change as the Jeep was running cool - they didn't do this as they said the diagnostic came up with transmission problems not engine ones. I don't know if I have the right codes but I'm looking for reassurance here. One of the codes was loss of prime or something similar, another was something to do with ratio on 1st gear out of alignment. Anyway, they said my EMS needs some flash updates, too. What I'm wondering is, am I screwed? Are transmission faults fatal? Is it likely the updates would sort out the faults?

The car is an 03 with 83,000 miles on it 2.8 CRD Ltd AUTO. Been good to me right up until now.

The dealer has asked to have the vehicle for three days to do more tests which include draining some of the oil in the transmission to see what they can find. They said that worst case would be new transmission which would not really be viable given the jeep's overall value.
What does anyone think?

What would I experience if there really were these kinds of faults? To me the transmission has been fine and not something I would have thought was a problem. I've no onboard dash lights coming on - would that mean it's not too serious? I'd hate to right the truck off but a new transmission would probably be way too much to throw at it.

Thoughts, help, reassurance?

I think one code was:
P0731 Gear Ratio Error in 1st
P0944 or P1791 certainly said Loss of Prime but not sure which code.

When is the last time the ****** fluid changed . What are the sounds or ****** doing. Slipping ,shuddering ect. And no factory updates. Need info.

Transmission may only need a drain, flush, replace filters, re-fill.

I believe you have to do a 're-learn" procedure after doing the above.

You will obviously have the "Euro" torque converter....the envy of USA KJ owners!