If the proceeds from the sale of the stock was reported to you on Form 1099-MISC, do not enter it (or delete it). It is an asset sale, and should be reported as such. The worst case is you get a letter from IRS saying you didn't report the 1099-MISC. If this were to occur, you would just write back and explain that it was for the sale of stock, and you reported the proceeds on Form 8949 and Schedule D (and enclose copies of those forms).
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