Merlinscribe: The Journal of James P. Mallory

While the Nine Shrines (of which, in toto, there are 81) cannot easily be destroyed, they can be Tainted by dark magic (and thus rendered unusable), drained of power to the point they will require centuries (at minimum) to restore themselves, or simply rendered so inaccessible that most people can't get to them. Some of the Nine Shrines are natively inaccessible, such as those belonging to the Folk of the Sea and the Folk of the Air: unless one has fins and gills (in the first instance) or wings (in the second) these sites are inaccessible. The same goes for the Firefolk sites, which are deep in the Red Desert. And, of course, when the last of the race whose Shrines they are is extinct, those Shrines go dormant unless and until they link with a new people. I think Idalia mentions that one of the Shrines belonging to the race of Men has been transferred to another folk and is thus unusable, but I don't remember exactly where that's mentioned.

While the Shrines are nonce-named "Nine Shrines", the "Nine Races" are actually composed of more than nine sentient species, and this taxonomy excludes the Brightfolk. (Runacar finds this especially annoying.)

So when Idalia says "Most [of the Nine Shrines] had been erased in the aftermath of the Great War", it must be noted that the Shrines originally stretched from Great Sea Ocean to the Cold Sea, and a great deal of that landscape was turned to dust in the Second Endarkened War, so presumably those Shrines in the wasteland areas were either Tainted or drained of power.

Of course after the Great Flowering of Kellen's time, all of those Shrines were both cleansed and restored, so as the population of Jer-a-kaliel expands eastward, many of them are likely to be rediscovered by those races they originally belonged to.

I hope this helps answer your questions.