Are calcium and magnesium lost by soaking beans?
See Common Bean Myths from Captious for a survey of several bean related issues.  They report that Cook's Illustrated has indicated (emphasis added): 


  [...] during soaking many nutrients leach out of the beans, more so with a quick
  soak (presumably due to the brief heat) than with a long cold soak.
  Apparently heat breaks down cell membranes within the beans, and
  increases the solubility of water-soluble nutrients, such as calcium,
  magnesium, thiamine, riboflavin, and niacin. As a result, quick
  soaking tends to leach somewhat more of the nutrients out of the beans
  than do slow soaking methods.