I would recommend setting this up in Solidworks Simulation (not Flow) initially. You can define heat generation as a function of the battery temperature (Thermal Loads -> Heat Power -> Temperature Curve). Setting up the curve does require some effort but I think it will allow you to understand the problem without getting into a complex Flow Simulation. Just my opinion.
Also, you may want to run this as steady state initially and then switch to transient when you are comfortable with boundary condition, etc.
Thank you for your answer, I will try to do what you explained.
I will also run the Flow simulation with the average heat losses in steady state to see if everything looks OK.
I already ran some calculation in transient, and the results seem quiet good when comparing to real tests, only thing is that it takes a very long time and I think I cannot go with a lower timestep or a lower mesh.
Again thank you for your answer, I am also going to send an "improvement demand" to SolidWorks to see if this can be solved directly in the next FlowSimulation update (or the next one ;-) )