I have a vested and timely interest in this topic, because I'm sitting here with a box of tissues, a cup of herbal tea, and a blood elderberry level over the legal limit, as I deal with a nasty late-fall cold. And I can also feel a couple of recent injuries, obtained through overuse and overzealous martial arts practice, more acutely than usual. This is above the usual attendant joint pains. Although pain is a complex thing to assess, I have some idea of why this might be happening in my case. It's a flare-up which is well-known to both science and many people who suffer from it.
For one thing, it's extremely useful to realize that pain doesn't necessarily mean damage. Oftentimes, when pain from an old injury returns, we think that we must have "re-injured" it. While this can happen, it's also often the case that our body is just trying to protect itself from getting hurt - your nervous system remembers the injury on some level, and as the adage goes, "Once bitten, twice shy."
Most people probably don't think they have re-injured themselves when getting sick causes old pains to mysteriously reappear. But there's a similarity here: the nervous system is on general high alert! In this case, it's being primed by the immune system, which is racing to defeat the invader, like a fire truck with its sirens screaming, roaring out of the station. Your nervous system then acts like the station's resident dalmatian, instinctively barking and howling furiously in chorus with the fire truck.
In fact, the links between our immune system and our nervous system can be incredibly tight - there are immune cells sitting in the junctions between our nerves, putting out little signals that either ramp up or ramp down the transmissions between the nerves. In the case of systemic inflammation, the signal is ramped up, like using a bullhorn to shout at your neighbor's house - it's a good way to get a message across, but it might be a little blunt! So, danger signals that may have been too quiet to alert your central nervous system before are suddenly getting your attention.
So what to do about it? One thing is not to worry too much - like those tests of the tornado sirens in Midwestern towns, these aches and pains are more annoying than anything. Still, we don't want to needlessly aggravate our nervous system and potentially prolong the pain. If you have significant pain in a joint, for instance, you may want to move it around gently and slowly when possible, to desensitize ourselves to the movement and reduce pain. Vary your movements, breath gently, etc. If you are fatigued like me right now, slow and gentle sounds great anyway! Avoiding movement altogether is not usually recommended outside of acute injuries, so do get up and about a little bit at least.
Being sick is just one of those great times to slow down, contemplate things, and realize how great it will be to get better again!