To give you what really happened that night, I would know, I used to work on them myself, sweet aircraft to work on. Just a pain in the rear to get to any panel due to the coating.
That night we lost that F-117a, was not due to the enemy tweaking there wavelengths as you say, it was due to a malfunction on the aircraft itself. After the pilot dropped his bombs, one of the bomb doors failed to close, that itself made the aircraft light up like a X-mas tree on enemy radar, and that's the only reason that the aircraft was shot down.
Also, for the reason why they retired the aircraft, its not because they are not stealth or not invisible. It was due to the age of the aircraft, these F-117a were never designed for a long term aircraft. Their air frame hours life was about 4000 hours I think, but was extended over and over due to the need for the aircraft, and the other reason for its retirement was due to the cost to fly them was expensive.
But the 5 years I worked on them was some of the coolest years in my career.