Magnetocapillary interactions between particles allow to self-assemble floating crystals along liquid interfaces. For a fixed number of particles, different states possessing different symmetrical features, known as metastable states, coexist. In this paper, we demonstrate how to trigger the transition from one state to another, either by rearranging the crystal, or by controlling its growth. First, we show that externally controlled magnetic fields can squeeze the entire crystal to induce structural modifications, that upon relaxation can lead to a modified state. Second, we propose localized laser-induced thermocapillary flows that can be used to guide new particles towards an existing crystal in a desired direction, thus favoring a particular resulting state. The control of the formation of metastable states is a key ingredient to functionalize such assemblies, paving the way to self-assembled microrobots.