My impression was that they aren't jack hammering to lower the height, rather they need to expose the rebar cage to give the new pour material the necessary bonding and reinforments. I think at least some of the piers are too low in height and they actually need to raise the elevation. (New KCCI info indicates as much, although it sounds like elevations at all piers and ramps at either end are all over the place.)
The other aspect is the anchor bolts and embed plates were mislocated (or missing altogether), so they would need the fresh concrete at the top in order to place those critical elements.