The situation you describe is a bit different because the answer does not have to do with thermodynamics (enthalpy and entropy), but instead involves kinetics.
It is incorrect to say that filling the vacancies is endothermic (I assume you mean endothermic here). If you compare the energies of a metal with vacancies to the enthalpies of metals without vacancies, you would find that the metal without vacancies has a lower enthalpy (i.e. moving a metal atom into a vacancy gives a more stable state). Even though you need to heat the metal in order to get the atoms to fill the vacancies, you have a net release of energy and the process is exothermic overall. A similar situation is the combustion of gasoline in your car. Even though you need to provide an energy input (a spark) to ignite the gasoline, you end up getting more energy out from the combustion than you initially put in.
So, what is the heat doing in your example if it is not going toward increasing the enthalpy of the metal? In this case, it's providing the activation energy needed for the necessary rearrangements to occur. In order to fill vacancies in the metal, you need to first break some of the chemical bonds in the metal, a process which requires an initial input of energy. This initial input of energy is the activation energy. Of course, when the bonds re-form and fill the vacancy, you will form more bonds than you started out with, and therefore, the process will release more energy than the activation energy you put into the system.
The type of system you describe is referred to as a meta-stable state: a non-equilibrium state that will persist for prolonged amounts of time. In this case, the system is trapped in this meta-stable state and cannot relax to equilibrium because the reactions that rearrange the atoms to fill the vacancies are too slow at room temperature. Only by heating up the metal can you get these reactions to occur at a non-negligible rate and allow the system to relax to equilibrium. Because it is the kinetics of the reaction (the speed of the reaction) that lock the system into a non-equilibrium state, we would refer to this state as a kinetically trapped state.