We present a model of synchronization in networks of autonomous agents where the topology changes due to agents motion. We introduce two timescales, one for the topological change and another one for local synchronization. If the former scale is much shorter, an approximation that averages out the effect of motion is available. Here we show, however, that the time required for synchronization achievement is larger than the prediction of the approximation in the opposite case, especially close to the continuum percolation transition point. The simulation results are confirmed by means of spectral analysis of the time-dependent Laplacian matrix. Our results show that the tradeoff between these two timescales, which have opposite effects on synchronization, should be taken into account for the design of mobile device networks.