Answer 1: Pretty sure there is a Reconcile feature in Q2013 for investment accounts. Either Account Actions or a gear in the upper right corner of the register should show that feature.Answer 2: Go to Investing > Portfolio and click on the account, then click on the + sign next to the stock in question. That will give you the remaining "lot".It's possible you have fractional shares you need to dispose of. You can either go back to the final sale of that stock and adjust the shares, including the fractional shares, or you can go to that account register and select "Adjust share balance" from the Enter Transactions button.
There is no Sell All option.