if he is close enough to the surface, drag the workbench over to him, flip it over, and disassemble him
you can also get under the floor of the base through a >>>> minor spoiler >>>> collisionless triangle in the floor of the porch outside, next to the window which you may need to do anyway as a piece may spawn under the floor when you disassemble it
you will also likely want a second kerfus anyway in the future though, so if this doesn't work or you still lose a part or two, it's not a total loss. Just try not to sleep when kerfur is working for now.
