The total work done by all forces acting on an object throughout the motion interval of interest is what the work-energy principle involves. It never says "no forces are doing work." And it doesn't talk about changes in potential energy. The changes in potential energy are involved in the work done by the conservative force attached to the particular potential energy. The bookkeeping of work, (force and direction and distance), can become tedious in some situations, but it works.
Let's say a person lifts a stationary box from a floor, carries it somewhere in the same room and sets it on a table. Let's also ignore air resistance, etc. The initial KE of the box in the table/room/floor reference frame is zero. The final KE of the box is zero. The total work done by all forces acting on the box is zero.
What forces did work on the box? AHA! The normal and frictional forces of the person's hands initially did positive work (force is up, motion is up), then more positive work as the person exerted a sideways force with sideways motion, and finally some negative work as the person exerted upward force to gently place the box on the table rather than dropping it. Gravity initially did negative work (gravity down, box moves up), and zero work as the box moved sideways (ignore the slight bouncing of the box while it's being carried) then positive work while the box moved down. All this work on the box adds to zero.
Meanwhile, the heart and brain and muscles were all doing work internal to the person, so they had to go get a soda pop and sit down and rest.