Is it that simple?
No. It's even simpler. Replace your rope with a motionless brick, lift it up, and put it on a shelf. It started with no kinetic energy, and it finished with no kinetic energy. But you did work on it, you added energy to it, and we call it gravitational potential energy*. As a result the mass of the brick increased a little. Then when you nudge the brick off the shelf it falls to Earth. Potential energy, or internal kinetic energy, is converted into macroscopic kinetic energy, and once this is dissipated you're left with a mass deficit. Have a look at mass in general relativity and you will appreciate that this simple little situation is lugging some baggage: invariant mass varies! And not only due to gravity: the mass of a hydrogen atom is less than the mass of a free electron plus the mass of a proton. The electron, and to a lesser extent the proton, has lost mass.
*Strictly speaking we should talk about the Earth-brick system, but the motion of the Earth is not detectable, so we simplify matters by focussing on the brick.