I've had lupus for the last 14 years and I am currently having kidney involvement. I am on cytoxan treatments monthly and will say that once they get it under control the flare ups won't always affect the kidneys. I was on cytoxan years ago and after the docs took me off of it I would just have my normal flare up symptoms.... achy swollen joints, etc. The kidney problems were not as prominent. My flares tend to change with the the weather: pleurisy during the winter months, swollen joints when it rains...
So I guess to answer your question, lupus won't always affect the same areas all the time. You may have problems with your kidneys now, for example, but subsequent flares won't necessarily involve your kidneys.
Hope this info helps.