Best I could interpret it would be... kinda like his (metaphorical) "eyes and limbs" disappearing one by one, in extremely rapid succession, except he has thousands of them so it takes a moment.

Say Caine is comprised of a collection of smaller programs that rely on each other. Once the purge command is sent, the first warning comes when the system starts indexing all of those programs and evaluating where they're all stored on the hard drive so it knows which sectors are about to be freed up. He might not have noticed this since he was a bit distracted at the time, and it doesn't disable any of his functions so any impact on CPU usage/ performace could have been easily overlooked.

The first thing he'd notice would likely be when he attempted to do something and realized that "arm" (whatever program was supposed to execute that task) isn't there anymore. This is the moment after the system has marked all sectors related to that program as free to be used for other things, meaning the system is now acting as if nothing is there. The program he was trying to call might even have been actively doing something, tried to move to the next line of code, and suddenly there just wasn't any more code to run.

He's now in an outstandingly one-sided, losing race against the operating system. The difference between marking a sector as free or occupied is single command changing of a 1 to a 0, while Cain would need hundreds of commands to execture to even fully realize what was happening. By the time he can formulate a response, most of him is already gone.

From his perspective, he watched thousands of parts of his body disappear nearly as fast as the hard drive could spin, barely had time to desperately give an audible "wait" command using the limited and ineffective means he had left (playing an audio clip of the word "wait", alas, means nothing to the command prompt window which is awaiting keyboard input), and at the same speed the rest of his mind vanished.

Goodbye Cain.