The simple answer is that any excess capital losses essentially die with the decedent; they cannot be transferred to the estate.
If the loss was incurred as a result of a sale that was effected after the decedent passed, then the loss would be recognized either by the estate or the trust (whichever entity owned the asset).
EDIT: Since you made a 645 election, the loss would be recognized by the estate since the trust is treated as a part thereof (again, assuming the sale was after the decedent passed).
