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It depends on how many. Nowadays what's commonly done is "sentinal node biopsy" which means injecting dye or radioactive tracer (or both) to see which lymph nodes drain the area in question, and removing only those. Side effects are very low in that case; they still can occur, and include swelling of the arm and nerve injury. If more are removed, the chances go up. Sometimes, depending on the nature of the calcifications and the tissue in which they are located, it's not possible to get a reliable analysis during the surgery, and the decision for lymph node surgery is made later, if a diagnosis of invasive cancer is confirmed.
I am concerned about the sentinel node biopsy reccomendations. I have a friend who went through a clinical trial and her sentinal node showed no signs of cancer but there was cancer found in two of her nodes. I was going to do the sentinel but I thank God my surgeon insisted otherwise.