The main reason is that while we are asleep, we are making fewer demands on the body, so that it can now use the bodies resources, to tame the flare. Rather than use them all up, to try and let us do our day to day tasks, since we are up and about. Resources are finite on any given day when you have FM, but during a flare, they are almost nonexistent.  

A little stroll here, through the inner workings of the body, to explain this.

What are body resources ? 

Energy to rebuild, which are created by a variety of things. Lipids ( fats ), Carbs and Proteins. Most of which come from calories burned from food, which depends on a gut that is A: Processing things correctly and B: Passing the energy onto the blood stream. The O2, from the lungs which is, one hopes, passed into the blood stream, to activate all of the above, as all cells need oxygen just to live, much less to work. So, to DO anything at all, on any given day, a lot of things have to be in working order.

How we get energy from food:

"Our digestive and nervous systems facilitate the ingestion of food and contribute the enzymes that break down sugars and starches into glucose. The endocrine system contributes insulin which, along with glucose, is delivered to cell membranes via the circulatory system.

Once it is inside the cell some glucose gets converted to glycogen — a storage form of glucose — that acts as an energy reservoir. The rest is delivered to the batteries of the cell called mitochondria. Each microscopic mitochondrion contains hundreds of enzymes with highly specific tasks. As each enzyme does its work, a chemical reaction causes breaks in the chemical bonds of the glucose molecule producing a different glucose derivative until the original molecule has been fully degraded to the components from which it arose in the plant — carbon dioxide and water.

Understand however, that even on a normal day, we stand at what is called the "lactic" threshold, in our muscles. ( Which translates into, they are two cents off of total collapse, as if we were pumping iron all day ) and since our muscles comprise our major cellular mass, the body will find slim pickings in that area if it wants energy, along with, some major demands being made of the blood cells by those very same body parts.

( For which Mycoplasmic infection on site link, may well be to blame )  As according to studies on the effects of FM, the mitochondrial cells, which are the cells that contain the lipids, which make energy for muscle tissue to use, are being damaged, therefore the muscle cells themselves, are being damaged as a result.

So if the blood cells have to go hunting for energy, as the body has little to spare floating around in the blood stream. the cells of the muscles literally cannot, not even to help themselves, provide that energy. It's like they are so tired, that food might be within reach, and they don't even have enough energy, to lift  "a cellular hand" to reach for it.

The idea of  processing  food correctly, is really put into question, as most of us have IBS as noted above, over 80% of us and we often stand at what is called "caloric exhaustion" at any given point, regardless of the diet we eat. So our digestive system, does not work well for energy processing either. Which is why the situation above, of there being little of free energy in the blood stream, happens in the first place.

Then of course the O2 exchange, which is vital to all of the cells in the body, is often compromised, as most of of us have shortness of breath, for a variety of reasons, from the mechanical ( the rib cage and chest muscles themselves, that make it hard to breathe ) and or have COPD or other issues. Even at a cellular level, we are shown to have poor oxidation of the cells, even when there is normal intake and exchange of air.

Which means, that even with all the air in the world to breathe, and a proper diet, the body still can be standing there, doing without, on a chronic basis. And when it is pushed too far and too hard, the signs of the disease increase and we have what is called a flare, creating an even greater demand, that the body often has little to no freely available resources, to try and fill.

That being the case, the body uses up what few resources are normally available, in very short order during a flare.

However, more is still needed, so the body goes hunting for it, most often taking it from the bones, the teeth, hair, anywhere it can find things that it can convert into usable body resources, to repair the damage being done. In short, it is the body, basically feeding on itself during a flare.

This fact is why most of us have low density in our bones, often have poor teeth, straw like hair, thin brittle nails and damaged skin. It is also is why during such flares, every alarm bell we have, are all ringing at once. As the body is on full alert, doing some rather extraordinary things, just to try and minimize damage and allow for some functionality, but it is often stripping the body almost bare, to do it.

So the bottom line is, often the best thing we can do, to help the body along, and ease our own pain, and prevent as much damage as possible, is to feed the body as best we can and then sleep. Sleep and let the body do what it does best, which is heal what it can. Without us, making more demands on an already overtaxed system.