Upgrading old worlds affected by MC-2545 & MC-4061 causes the world to become unplayable

Worlds created between 1.4.4 and 1.8 may have misplaced chunks due to MC-2545
Inside those chunks there can be thousands of entities due to MC-4061
Between 1.8.1 and 1.12.2 these bugged entities would be properly removed letting you load the world as normal, but since 1.13 this is no longer the case.

Upgrading these worlds will take a long time (this report previously stated forever, but this is not actually the case as it turns out) and once you load in the world will be completely unplayable due to the intense lag.

Reproduction Steps

• Put this world in your saves folder

• On version 1.21.1 try to enter the world or use the "optimize world" button

• Wait several minutes for the world to upgrade

Observed Result

• The internal server stops after a few seconds

• Looking at chunk -27,28 will cause your FPS to spike
  

  [media]

After using the performance profiler I realized chunk -27,28 contains a stupendous amount of skeletons due to MC-4061. About 13 thousand.

Expected Result

• Entities in misplaced chunks would be cleared as was the case in 1.8.1 - 1.12.2