The Chandra observations of several gravitationally lensed quasars show evidence for flux and spectral variability of the X-ray emission that is uncorrelated between images and is thought to result from the microlensing by stars in the lensing galaxy. We report here on the most detailed modeling of such systems to date, including simulations of the emission of the Fe K-alpha fluorescent radiation from the accretion disk with a general relativistic ray tracing code, the use of realistic microlensing magnification maps derived from inverse ray shooting calculations, and the simulation of the line detection biases. We use lensing and black hole parameters appropriate for the quadruply lensed quasar RX J1131-1231, and compare the simulated results with the observational results. The simulations cannot fully reproduce the distribution of the detected line energies indicating that some of the assumptions underlying the simulations are not correct, or that the simulations are missing some important physics. We conclude by discussing several possible explanations.