Holes in worlds created in Alpha and Infdev below y=0 after conversion

I generated a world in Minecraft Infdev and converted it through the versions to simulate a legacy world being gradually updated with time and eventually being converted to the latest snapshot, the result (besides the incorrect level of water, of course) were these huge empty shafts in the newly generated layers of Deepslate and Bedrock below the Infdev map. The rest of the world looks fine, the transition between infdev and 21W43A terrain also looks fairly smooth.