Has a commercial passenger airliner ever had its cockpit fully upgraded?
While many times an upgrade is not economical for older airplanes, sometimes the new features make it worth the cost.

Two examples I found were Southwest upgrading their 737-300 fleet, and Delta upgrading their MD-88 and MD-90 fleet. The second article also mentions American and Icelandair 757 and 767 upgrades. The Southwest and Delta upgrades involve over 100 aircraft in each case, which probably helped to make the upgrades more economical.

In both cases, a major factor mentioned was the ability to perform required navigation performance (RNP) procedures with GPS and other modern features. As the FAA works to implement the NextGen ATC system in the US, these upgrades will offer more benefits for the operators.

Also, I'd like to comment on the following statement:


  Concorde was not properly maintained as its analogue flight deck had never been upgraded.


Proper maintenance and technology upgrades are not always the same thing. Aircraft with older systems can be maintained just as well as newer planes. We have airplanes that are 50 years old or older, like the DC-3, which are still flying. While technology upgrades certainly have benefits, aircraft with analog cockpits are still operating just fine around the world. They may not be the most modern machines out there, but proper maintenance is what has kept them flying this long.