In a recent paper (El Omari and Le Guer, IJHMT, 53, 2010) we have investigated mixing and heat transfer enhancement in a mixer composed of two circular rods maintained vertically in a cylindrical tank. The rods and tank can rotate around their revolution axes while their surfaces were maintained at a constant temperature. In the present study we investigate the differences in the thermal mixing process arising from the utilization of a constant heat flux as a boundary condition. The study concerns a highly viscous fluid with a high Prandtl number $Pr = 10,000$ for which this chaotic mixer is suitable. Chaotic flows are obtained by imposing temporal modulations of the rotational velocities of the walls. By solving numerically the flow and energy equations, we studied the effects of different stirring protocols and flow configurations on the efficiency of mixing and heat transfer. For this purpose, we used different statistical indicators as tools to characterize the evolution of the fluid temperature and its homogenization. Fundamental differences have been reported between these two modes of heating or cooling: while the mixing with an imposed temperature results in a homogeneous temperature field, with a fixed heat flux we observe a constant difference between the maximal and minimal temperatures that establish in the fluid; the extent of this difference is governed by the efficiency of the mixing protocol.