The non-linear dynamics of large ion clouds trapped in radio-frequency traps, coupled to laser-cooling, give rise to a bistable behaviour concerning the equilibrium temperature. Numerical simulations of the free evolution of a large three-dimensional cloud is used to characterise the parameters controlling the switching between two stable states. They are used to design scenarii to control the thermal state of ion cloud with large Mathieu parameter and to take advantage of the threshold effect to detect and quantify perturbations by an intruder.