When you took your lump-sum distribution, If, as you said earlier, the only assets remaining in your 401(k) were shares of company stock then you should have only received one Form 1099-R, and you only need one 1099-R. Using your example above for a $10,000 distribution of company stock with a cost basis of $4,000, your original 1099-R was correct and should be entered that way. You should NOT indicate that you rolled any of the funds over. If the lump-sum distribution was done properly it was all distributed to a non-qualified brokerage account, not an IRA or other retirement plan - this is not a rollover. The $4,000 in box 2a should show up on your tax return as taxable income. The $6,000 is your cost basis in the shares distributed. This amount does not flow to your tax return. Your broker should use it as the cost basis for your distributed stock.
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