Note in the Figure of Project 21956 attached to Page 12 of the Russian Navy News & Discussion, Part III that 40N6 is reported with a mass of 2.000 kg and a top speed of 2.3 km/s. Another source claim the 40N6 mass is around 2.200 kg. So, in the end the “Big Missile” is likely an evolution of the 48N6 family rather than a 2-stage weapon, as it was speculated some time ago.
The evolution on the top speed seems also to confirm this hypothesis. From 2 km/s of the 48N6E (S-300PMU1) to 2.1 km/s of the 48N6E2 (Favorit system), to 2.2 km/s of the 48N6DM (early S-400 system) to 2.3 km/s of the 40N6.

So the replacement of older 48N6E missiles by 40N6 in Russian cruisers should not be difficult at all since 40N6 is a stockier 48N6 with an active seeker likely carried in the same canister type.