The answer is that no one removed them and they're still there, under the capital. Many of the old stocks were used during the Battle of the Blackwater, but there are still a lot of jars of the stuff, unused, under various parts of the city. read more
No one alive - except Jaime Lannister (and Brienne) - knows that Aerys had wildfire caches planted all around King’s Landing. Jaime killed Aerys and the three pyromancers who were the only ones who knew where the caches were. AFAIK, even Jaime doesn’t know their locations, just the fact that they are there. read more
I was under the impression that the wildfire used in Blackwater was created after Roberts rebellion then even more so when Cersei had commissioned the pyromancers so the thousands of jars would still be under the city. read more