How do I handle a stock sale with both LT and ST amounts (and different basis) in TurboTax?
The broker will breakdown the sales into ST & LT on the 1099-B based on the time you held the stock after the distribution. Each share of stock will have a cost basis that you have already paid taxes on it in the year of distribution. One share of stock sold cannot be both short and long term at the same time(or broken out by percentages).
So say you have 100 shares in company stock to move and you originally bought 10 shares (@$10 each ) and are taxed on those 10 shares at distribution (on the 1099-R) that means you now have 100 shares worth $1 each. So the cost basis in all those shares are $1 each.
So ... if you have 100 shares and you sell 10 before a year has passed then all 10 shares are considered short term sales. Then any stocks sold after one year are long term sales. If you broker doesn't break down the sales for you then you will need to do the math and enter the sales into the program manually.
Shares distributed in-kind from retirement accounts are often (perhaps always) recorded the broker as uncovered shares, so there's a good chance that the broker will not report a cost basis for these shares. They might also report these shares as having an unknown holding period.
Ultimately your tax return must report the correct dollar amounts of LT and ST gains. One way (perhaps the only way) to do that would be to enter each share twice as you suggest, LT with the sales proceeds equal to the value on the date of distribution from the 401(k) (the share value reflected on the Form 1099-R) and the actual cost basis (also determined from the Form 1099-R by subtracting the NUA from the share value) and again as ST with the sales proceeds equal to the value on the date of the sale and a cost basis equal to the value on the date of the distribution. It's the method that I thought of independently before seeing that you had suggested the same thing.
Using this method with your example, yes, you would report a LT sale of $100 with $50 of cost basis and a ST sale of $110 with a cost basis of $100, resulting in $50 of LT gain and $10 of ST gain on Schedule D as you indicated. My only concern is whether the reporting on Form 8949 which will show what the IRS expects to see under these circumstances. I would probably include an explanation statement with my tax return describing this sale and why the sale appears twice on From 8949. I have not been to find any guidance from the IRS on how to report this.