Yes, you can.
If the cost basis information is incorrect in your downloaded (imported) data, then you can go into the input screen and manually input the correct cost basis.
To do that,
1. Click Show More by Investment Income on the Income & Expenses menu.
2. Click Revisit by Stocks, Mutual Funds, Bonds, Other
3. Click Edit by the brokerage name.
4. Click Continue.
5. Click Edit by the brokerage you'd like to change.
6. Click in the field by Cost Basis.
7. Click Done till you get back to the Income & Expenses menu.
Make sure you keep a record of how you computed your cost basis with a copy of this year's tax return.