The process of diamond and gemstone recovery from karat gold jewelry scrap is far more complex and time consuming than a direct melt and assay recovery. Jewelry that contains recoverable diamond and gemstone melee will always yield a much higher value, as long as the refiner you choose is implementing sound wet chemistry processes that minimizes the potential for mechanical losses of metal and damage to the your valuable gemstones. You should expect the refiner to charge higher processing or treatment fees for this service as well as allowing a little more time for final results but in the end, the additional value you'll receive back from the sale of your stones more than justifies any inconvenience.
Several years ago I wrote an article for PawnLink.org that highlighted the growing frequency our pawnbroker customers were being exposed to and taken advantage of with fake bullion and replica coins. Many of these defrauded, poured, and extruded Precious Metal investment pieces started out as legitimate bullion products coming from reputable refineries and banks. Scammers would drill out actual Gold or Silver from these pieces and back-fill them with materials like Lead or Tungsten rods. Eventually, we began seeing scammers implementing higher levels of skill to produce replica coins and bullion through minting, electroplating, and even cladding over low value base metal to look like authentic precious metal currencies and investment bullion.