EX Lup is the prototype of a class of pre-main-sequence eruptive stars defined by their repetitive outbursts lasting several months. In 2008 January─September EX Lup underwent its historically largest outburst, brightening by about 4 mag in visual light. In previous studies we discovered ongoing silicate crystal formation in the inner disk during the outburst, but also noticed that the measured crystallinity fraction started decreasing after the source returned to the quiescent phase. Here we present new observations of the 10 μm silicate feature, obtained with the MIDI and VISIR instruments at Paranal Observatory. The observations demonstrate that within five years practically all crystalline forsterite disappeared from the surface of the inner disk. We reconstruct this process by presenting a series of parametric axisymmetric radiative transfer models of an expanding dust cloud that transports the crystals from the terrestrial zone to outer disk regions where comets are supposed to form. It is possible the early Sun also experienced similar flare-ups, and the forming planetesimals might have incorporated crystalline silicate material produced by such outbursts. Finally, we discuss how far the location of the dust cloud could be constrained by future James Webb Space Telescope observations.