Backup your world.
Spawn in a filler, and set it to clear.
Spawn in a redstone energy cell and start clearing the hell out of your base (make it 64x64, as big as it can get).
Find sheep, go to its coordinates and copy them down.
Go to your backup.
Go to coordinates.
Make warded stone cannon like this:
F = Nuke
E = Warded Stone
FEEEEEF
FEFFFEF
FEFFFEF
FEFFFEF
FEFFFEF
FEFFFEF
FEFFFEF
FEFFFEF
FEFFFEF
FEFFFEF
FEFFFEF
FEFFFEF
FEFFFEF
FEFFFEF
FEFFFEF
FEFFFEF
FEFFFEF
FEFFFEF
FEFFFEF
FEFFFEF
Ignite the nuke and run like hell. The explosion will go directly downwards and obliterate anything in a 1x1 (it will expand towards the bottom, sort of like a trumpet shape) column all the way to bedrock. Or close to bedrock.
Your sheep problem is now fixed.
Just ignore the giant cylinder of nothing. Try not to step in it, it'll be a long fall.