It is actually more the rule than the exception that the substance of the very old historic (medieval or older) structures of Europe is mostly rather young - reconstructions, replacement or modern additions. Just take the spire that collapsed today: It was actually only built of oak wood in the 19th century. Take the gothic cathedral in Cologne, Germany's most visited landmark, construction of which began in 1248: Its famous towers, at more than 157 meters the tallest buildings in the world until 1884, rose above roof level only after 1842 and were completed in 1880. The crumbling stone of the facade has been renovated so often and so much that I doubt much of what you see today originated before 1322, when the cathedral was consecrated. Fires and wars have laid ruin to many monuments that have subsequently been rebuilt - and many are billed as "medieval" or somesuch.
In the case of the cathedral in Cologne, it's that Master Gerhard, the first master mason, made a bet with the Devil that resulted in that it is cursed never to be finished.
Myth aside, the reason it was 'finished' that late is because they ran out of money until people decided it's worthwhile to raise money for it. Notre Dame was similar in that as it was in major disrepair after the revolution, and in fact Victor Hugo's Hunchback was quite influential to raise the money for its rebuilding.
I put 'finishing' in quotations above, since it's my understanding that all buildings of that size and age need constant maintenance, rebuilding, and replacement. They are never set in stone, so to speak, but are living entities.
The cathedral in Cologne has it worse in that regard as it has one of Germany's largest railway stations as its immediate neighbor. There's scaffolding attached to one of the towers, and from what I know it's unlikely to be ever without that scaffolding. It will just move about the structure to another area in need of maintenance.
One of the good things of all of that is that in almost all the major landmark buildings there is extensive documentation. I know that the original plans for the cathedral of Cologne and Notre Dame are preserved, digitized, and backed-up. I know that Notre Dame, like the cathedral in Aachen, has just been extensively digitally scanned. Which means that it can be rebuilt with very little visible changes, if there's a will and money. Which is different like other disasters like the collapse of the Historical Archives of Cologne in 2009, where documents were irretrievably lost.
Better than nothing.
