SOMA Enemies (major spoilers)

[kojack]

The only place he exists in the maps is that one spot in omicron. When you hit a certain trigger area the script calls a function described as:

// Scene 5 - Misc Spook Events - Patchwork man disappears

which just removes him and turns off the distortion effect in that area.

The trigger is at the door at the top of the stairwell that is next to the patchwork man. So it happens on the way to the chargepack, but the chargepack isn't the cause.