BOSTON — An audit of the Boston Public Library says it ineffectively protects its special collections, haphazardly stores valuables, and does not keep a complete inventory of prized possessions.The audit, obtained by The Boston Globe was given to the Boston Finance Commission on Tuesday. It comes just weeks after two valuable pieces of art worth $600,000 were reported missing, and possibly stolen.The audit says the library used guesses to estimate current holdings, often based on guesses made years ago.