For more information, refer to How to add stock/property gifts and assign them a value (BB56038) and IRS's Publication 561.
Alternative solution for a stock gain:
Add a write-off to the pledge to reduce the pledge balance.
For example, the donor gives you stock valued at $100. You sell the stock two weeks later for $120. The donor feels like he should receive credit for the $120 rather than the $100. For tax purposes, he can only receive credit for $100. However, your organization can give him credit for the full amount. The $100 would already be applied to the pledge, so you would add a $20 write-off to the pledge to decrease the balance by an additional $20.
Alternative solution for a stock loss:
If the original stock amount is larger than the pledge, the user will be prompted as to what to do with the overage when applying the stock property sold to the pledge. Choose the first option to change the gift amount to equal the pledge amount without an overage gift created.
Choose the second prompt to create an overage gift and adjust the stock property sold amount to zero.
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