This is normal and to be expected. Just keep flushing at your own pace until the symptoms start to subside. Eventually you will start to feel better for longer periods of time until the whole biliary is cleaned out. A large dose of magnesium may be enough to dilate your biliary system enough to allow some of these new stones to pass, otherwise you will have to wait until the next flush.
You can try things like peppermint tea or oil, ginger, chamomile or castor oil packs. But until you clear all the stones out these things are just palliative. Sometimes juice fasting can be good in this case to avoid stimulating the liver. Chanca piedra also has a specific action of relaxing the smoothe muscle in the common bile duct and can provide palliative relief very fast.
Some people can flush more often than the two week waiting period, others not.