The sum of all energy (chemical, electromagnetic, kinetic, etc) in the universe is constant.
The energy which you observe is either lost or gained in a chemical reaction is chemical energy.
Let's consider an exothermic reaction. When it is lost, it is released to the surroundings as heat/light/sound usually. Heat, light and sound are alternate forms of energy. This is just conversion of energy from one form to another. Although chemical energy is lost, it is converted to another form(s), which has same the measure of energy. Hence, the sum of energy remain constant.
We only consider conservation of mass and energy in nuclear reactions, where mass and energy are inter-changeable. However, this interchangability does not apply to chemical or physical processes.