In his 2016 Handbook of Synthetic Organic Chemistry, Michael Pirrung wrote that yield is one of the primary factors synthetic chemists must consider in evaluating a synthetic method or a particular transformation in "multistep syntheses." He wrote that a yield based on recovered starting material (BRSM) or (BORSM) does not provide the theoretical yield or the "100% of the amount of product calculated", that is necessary in order to take the next step in the multistep systhesis.
Purification steps always lower the yield, through losses incurred during the transfer of material between reaction vessels and purification apparatus or imperfect separation of the product from impurities, which may necessitate the discarding of fractions deemed insufficiently pure.  The yield of the product measured after purification (typically to >95% spectroscopic purity, or to sufficient purity to pass combustion analysis) is called the isolated yield of the reaction.