When emptying (clearing all blocks) in a chunk, that chunk doesn't get saved upon reload.
To reproduce
Create a new flat world
Look around (This is to ensure all of the chunks loaded around you)
Dig one block down
Run the following command:
/fill ~20 ~ ~20 ~-20 ~-3 ~-20 air
Save, exit, then open the world
Expected result
The blocks between -20 -64 -20 to -20 -60 -20 should be empty upon reload
Observed
Blocks between 0 -64 0 to 15 -60 15 doesn't get cleared upon reload
Done some bit of testing and it seemed like it only affects chunks between Y=-64 and Y=-49