Here is a 'lay' version of what happens when something attacks our system.
Think of it like a battlefield....
When our bodies get sick and are under attack from an invader (say a virus or infection), our cells 'gear' up to hit back at the invader that is causing the sickness. In normal healthy individuals our bodies mount a cellular attack on the invader and if needs be, they 'call in' more and more cells, depending on what is being attacked and the strength of the attack, etc. Our bodies can call in help from many parts of our system including the T and B cells. Once the T Cells recognise the invader they start to multiply to fight off the attack.
When the invader has been disposed of, the T Cell army stands down its infantry and goes back into 'peace-time- mode busily keeping an eye out for more invaders. Thats what happens in normal immune systems.
However with Lupus we have a malfunctioning immune system. Once we have disposed of the Invader, instead of standing down the army that has just been built up to get rid of the invader, our out-of-balance immune system continues to generate attacks. Because the invader has long since gone, our army of cells has nothing left to attack but our own healthy tissue. This is what is called an auto-immune response and hence why we can feel really ill during flare ups.
I know this is very simplistic but it might help to explain why you feel worse during and after getting a cold or infection.
For me, a cold is almost always a mini version of the flu and I do find that my lupus flares up worse during and after the cold. I had been that way for years before diagnosis and thought my husband was very strange when he told me that for him a cold is contained strictly at and above the neck! I didn't realize it wasn't "normal" to have all those body aches with a cold.
My lupus will also flare up worse with a sinus infection, or the stomach flu, etc.