The difference between dissolving gold for refining and dissolving gold for stone removal is when doing stone removal it is to efficiently remove the stones, and for that efficiency the gold refining suffers. Often the silver content is too high for the gold to dissolve completely and the reaction leaves pieces behind. Usually the pieces are broken up enough for the stones to fall free but occasionally a soak in ammonium hydroxide followed by additional aqua regia treatment is needed. Some refiners will dissolve the silver chloride by tumbling in sodium thiosulfate solution. Both solutions are effective, some don't like the cloud the ammonia causes in the refinery so they choose thiosulfate. If your shop is messy and buckets of chemical solutions in different stages of processing are strewn about, I would stay away from the ammonia.
Generally speaking if the scrap can be melted, assayed bars are mixed to bring the silver content below 9 percent and the alloy is made into cornflake shot for digestion. The resulting chlorides will contain some gold, often 1% of the weight of the recovered silver. The chloride is simply reduced and melted into bars with gold as an impurity and processed in a silver cell. That way all of the gold is recovered eventually.
The difference is commercial refining does not use the inquarting technique often because of the lot size usually processed. Refining of karat gold in aqua regia can consistently produce gold in excess of .9995 fine and that is usually the path chosen by small and intermediate refiners.
