Adding you can add enrgy to a system without adding mass. Wind up trhe spring of a mechanical clock and you have added energy to the system but no mass.
I hold a baseball in hand. It has potential, kinetic, and nuclear energy. Total energy E = PE + KE + mc^2.
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I throw the ball in the air adding PE and KE. Total energy is still PE + KE + mc^2. Energy comes and goes mc^2 does not change.
You've got two responses disagreeing with this post. I'm not sure why.
There are other forms of energy than mass. If you heat up the box with the ashes in it, it will have more energy (in the form of heat) without having more mass. If you throw the box of ashes, you'll give it kinetic energy without increasing its mass.
This doesn't change the fact that chemical reactions involve tiny conversions from mass to other forms of energy, or from other forms of energy to mass.
Suppose a hydrogen atom absorbs a photon, thus raising an electron to a higher orbit. Does the atom then weigh more? I'm guessing that it does. The other form of energy is gone, and mass is what remains, so the mass of the atom should be increased by one photon's worth. I don't know this for a fact. I haven't read it anywhere. I'm just thinking it makes sense.
Energy is conserved. If energy comes out of your glass box when the paper burns, then the box contents will have reduced mass. This must be true unless the exiting energy comes from something other than mass. Your hypothetical doesn't mention any other energy source, and we know that burning paper is exothermic.
So the answer is that the chemicals in the box get lighter in proportion to the amount of energy escaping from the box.