If this is only two transactions (which is how I am reading your question to be), and there are two different cost basis amounts, I would imagine that the physical 1099-B would clearly state which cost basis belongs to which transaction, as well as properly categorize it as either S/T or L/T. If this is one transaction and you have two "cost" figures, then one of them should be stated as "adjusted basis" - and this is the one that you would use versus the one that should say "original cost basis". It truly all depends on these two scenarios I've laid out for you and which one applies to you. An adjusted basis it typically a "stepped up" amount to the original cost. An example, if someone inherits stock then sells it, they would not use the original cost of the stock as this most likely would cause a HUGE gain for them and thus trigger tax due. They would take the FMV of the stock at the date of inheritance, which in stock sales terms is called the "adjusted basis". I hope this helps.
