I think loading the checkpoint was the hardest part, since the code I had written up until that point was not designed for a scene reload, or saving & loading. It was supposed to be a game you just run through and not die in the middle, so when it came time to make the checkpoint I just sat there for about an hour trying to figure out what to do.
But yeah I essentially botched it and got it working. When the security grabs you and you load the checkpoint, the game basically restarts. The player spawn is moved to the computer, the toolbox is silently opened, the light goes red, the controls pop-up trigger gets removed and all of the first phase drill break triggers are removed, before the security alert starts again.
You'll notice that the drill isn't in the casing anymore & all the previous drilling lines are gone. Putting them back to the original position is almost impossible with how messy the code is.