In one embodiment, a hard-disk drive system performs fly-height control using a read-back mode and a loop-back mode. The read-back mode measures first and second harmonics pre-recorded on the medium and divides the first measurement by the second to obtain a read-back mode harmonic ratio. The loop-back mode measures the same first and second harmonics; however, the harmonics are provided by a write precompensation circuit rather than the medium. Further, the loop-back mode measurements are performed using asynchronous sampling to address aliasing and quantization errors. The first measurement is divided by the second to generate a loop-back harmonic ratio. In logarithm domain, the loop-back ratio is subtracted from the read-back mode ratio to remove environment-induced variations in the read path electronic circuits. The resulting harmonic ratio is subtracted from an initial harmonic ratio determined, for example, during manufacturing, to determine how much the harmonic ratio has changed.