In a chemical reaction or in a phase transition, the heat production or consumption rate is proportional to the rate of conversion. It is well known that the signal curve of a heat flux calorimeter is delayed and deformed. In order to obtain the true heat flow rate generated by the reacting sample, a transformation method is needed. This is often called "desmearing". There are two techniques for performing the transformation. Owing to its simplicity the method based on a linear second-order differential equation is preferred in this paper as a desmearing tool, rather than the method based on the convolution theory. There are two time constants in the transformation formula. The determination of these constants under real conditions is the main subject of this paper. For this, a comprehensive mathematical treatment of the problem is necessary.