The blog link describes the cleanup process.

They take two pictures, each taking up half the total observation period. If you subtract the two images, the deltas should be the cosmic ray flashes. You can then subtract those out. They use two pictures as opposed to more to minimize the impact of readout noise.

To deal with "stuck pixel" type errors, they can slightly shift the camera between the two observations. They can counter act the shift before doing the initial subtraction.

One way is to take a “blank” picture which will then show just the noise; then use that as a reference for what can be removed from the image.

its actually quite doable. any cosmic rays will not be present in two pictures in a row. any permanent damage will be exactly the same in all pictures.

photoshop ;D, or using multiple pictures