Well, the Cathedral itself was never the "same" throughout its history. Since it was first completed around 1190, Notre-Dame went to significant changes along the centuries, with its most recognizable stone structures, facade and the two bell towers being only completed at the end of the 14th century. No single European "Medieval" Cathedral maintains its original form in this current era, they were all upgraded, transformed, damaged throughout the years, etc, etc. Notre-Dame is not unique in this regard.
According to preliminary analysis of the damage, only the spiral and one-third of the roof were destroyed in the fire - those two structures were only constructed in the 19th century, they are not medieval. Most of the old part of the Cathedral, and its most emblematic structures, are still intact and didn't suffer any considerable damage.
What annoys me most is the media's tendency to show short clips in rapid succession to make the whole thing cheezy. However it can be definitely said that the windows that lit the attic of the transepts are gone. This is understandable. Above the vault the space was mostly enclosed which means there was very limited supply of Oxygen but it was rich in fuel (being the forest and all). This means shortly after the fire this place ran out of Oxygen and there were localized buildups of Carbon Monoxide (highly explosive). As the roofing began to give way atmospheric air entered these spaces, causing localized explosions called backdrafts. These most probably have been the culprits as the windows blew up outwards. However the main rose windows, I don't think have experienced anything like this as they are below the vault.
In this video 4.15 onwards it can be seen that smoke is coming out through one of these windows in short bursts. Also 6.00 onwards you can see the flames visible inside quite clearly (too clearly for the glass to be there). However I think a lot of people actually mistook these for the rose windows and the news spread more wildly than the fire itself.
I came across a report on AP that states that the organ has survived.
"Its iconic twin bell towers remained visibly intact. Paris officials said the world famous 18th century organ that boasts 8,000 pipes also appeared to have survived, along with other treasures inside the cathedral, after a plan to safeguard heritage was quickly put into action."
Fire brigade spokesman Lt-Col Gabriel Plus said: "The whole of the roof has been devastated... a part of the vault has collapsed, the spire is no more."
However, it could have been much worse. Mr Nuñez said that, had fire crews not entered the building, "without doubt it would have collapsed", French newspaper Le Monde reported.
Photos appear to show that at least one of the cathedral's famed rose windows has survived, although there are concerns for some of the other stained-glass windows.
Franck Riester, France's culture minister, warned that while the principal structure had been saved, the building was still unstable.
The damage, thankfully, seems reversible. Repairs will be costly and lengthy, but still, it seems completely feasible to deliver Notre Dame complete again.
May this serve as an alarm to tighten even more security measures for those special jewels of humanity. We can't allow not a sliver of chance to damage them - they are pieces of the very essence of human civilisation.