It would appear, according to the latest reports on social media that the great organ has miraculously survived the inferno. There is a photo of the west end of the building taken after the fire and it shows the front case intact, although how much smoke and water damage it has sustained is of course unknown at the present time. Not so much information as to the condition of the other organ in the choir is yet known, although in this case I would think that at least it must have suffered a great deal of water damage.
Although not really able to be classed as a genuine Cavaillé-Coll instrument anymore since it has been rebuilt many times, the great organ has a history that few other European instruments can match, For almost all of the major French organ composers of the late 19th and early 20th centuries have either given concerts here or have been appointed as the organist at one time or another. From the time that the young Charles-Marie Widor was chosen to be one of the organists to inaugurate the new organ in 1868, the list of organists read like a veritable Who's Who of France at the time when French organ music dominated the whole scene, probably with just a single exception, the German composer Max Reger.
I hear that President Macron has said that the cathedral will be rebuilt by 2024 but I think that's just wishful thinking. Another problem is just how are they going to replace some of the massive timbers that have been there for the last 866 years, because there are no trees of that size in the whole of Europe today, most of them went on constructing large sailing ships from the 15th-18th centuries. So these giant timbers that supported the stone walls internally will probably have to be replaced by steel RSJ's enclosed in wood to make them look authentic, but of course, all of this will need to be investigated once the full extent of the damage has been evaluated and the best plans on how to restore this iconic building have been decided.
As for the organ, let us hope that it can be fully restored in time in the same way and sound condition that had inspired so many organists and listeners alike throughout its history.
With best wishes,