dmo..
sorry..had to address something...if I read you right, besides an existing long postion still underwater, you have a side position that currenty has a gain. And you have a broker that designates or sorts shares by cost-basis...someone else brought this up last week. I use Scottrade and shares I buy of the same ticker at different cost basis' are up to me to sort as I see fit. Given your question I can apply the sale to loss (underwater CB) or a short-term gain but my broker does not designate it as yours might. If you need to tell the broker which shares to apply the new sale, it just depends on your trading status, the extent of the full 3K loss you might still want to claim on your Schedule D (if not a day trader mark-to mark status), or if you want to add to your top line overall in a given reporting year. All personal decisions that have to make sense to the investor. I may be reading you wrong, but if right, that's my take...
Strong action today gents (and ladies).. 
