Where does the energy lost due to light emission come from? If an object lose energy when it emits light, does that energy come from the mass of the object?
Examples:
Does a flashlight lose mass when it's turned on?
Does a regular object (like a pencil or a piece of paper) lose mass when the environment is colder than the object?
If there is a loss of mass, what specific part of the atomic structure does that mass come from?
Does it come from electrons (or other particles) losing mass? (in which case it would lead to some electrons having more mass than others?)
Or does it come from whole particles being converted to energy?
Or does it come from the kinetic energy of its molecules?
 A: When an object radiates heat or energy (without supply from external source), it goes into a lower energy state. There are different way for that to happen. I will take one example - the pencil one.
Think the reverse first - what happens if temperature of pencil is raised say by 10 degrees. The molecules in the pencil vibrate faster and gain kinetic energy. 
Same way, when temperature of pencil goes down by 10 degrees, it looses the kinetic energy of its molecules.
If you cool the pencil to close to 0 K, then in addition to kinetic energy of molecules, there may be other changes taking place in its structure, or orbit of electrons themselves. I am not sure, but I guess you get the idea.
A flash light looses energy because its battery chemical goes into a lower energy state by loosing energy.
The loss of energy can be considered a loss of mass per E = M * C * C. But it is not like a part of electron (or something else) break into energy.
Some nuclear decay kind of processes may/do actually emit mass particles though in addition to radiation.
A: You are being misled by some of these answers and responses. It is perfectly fine to think of the internal energy of the flashlight as real mass. Of course the percent difference in mass between a charged and uncharged battery is tiny but in principle that mass works like any other.
If you want a rough classical picture of where this mass is located think about the energy density of the fields. There is more energy in the field when a positive and negative charge are further away, and when they come closer some of this energy moves outward as an electromagnetic wave.
A: There is no general answer to where the energy for light emission comes from. Where the energy comes from ultimately depends on which physical process is used to produce the light. Blackbody radiation stems from thermal energy. A diode converts electrical energy into light. Electron-positron annihilation would indeed essentially draw from mass. And so on. 
A: Optical emission comes from (a) internal energy of the system, such as electronic excitation, or (b) external energy which stimulates the system, providing the energy which will later be emitted.
If the light comes from an otherwise closed system, and it emits total energy E, then yes, the mass of that system is reduced by $m=E/c^2$.
