Yes, if you have to upgrade to a higher level of the program, then you get credit for the first purchase and would only have to pay the difference between the costs for the two products since you already paid for the first one. When you go back to add the Form 1099-S, the program will prompt you to upgrade (it might indicate the full price - but, when you go to checkout, you should be charged only the difference).
For TurboTax Online, you can only prepare one tax return per account. So, you would need to use a second account to file your daughter's return. Its possible she may be able to use the Free Edition, however.
If you used the TurboTax CD/Download program, you can prepare multiple returns (e-file up to 5) with that software.