I have addressed the Baxalta / Shire transaction here:
https://ttlc.intuit.com/questions/3814587-can-you-help-baxalta-shire-merger-cash-and-stock
The transaction is fully taxable and you use the sum of cash plus
FMV of the stock as "proceeds" to determine your reportable gain or
loss. It's "as if" all the proceeds were paid to you in cash and then
you used some of the cash to buy Shire stock. Your holding period in your "new" stock starts the day after you received it.
Since you know the date of the purchase of your Baxalta stock I assume you know the cost basis too. The sale is being reported to you, I assume, as a Box E (or maybe Box X) trade which is saying that the cost basis is not being reported to the IRS. So when you enter the 1099-B you simply enter the cost basis from your own records at the same time, coming to a resulting gain or loss.
Tom Young
