The Sch D / 8949 input for 1041s is a bit anemic.  What you want on the 8949 is an adjustment code "L" and the amount of the adjustment equal to the non-deductible loss.

I would try entering the actual basis in I1 and the sale price in I2 "Corrected basis" but then you have to go to the 8949 and override the code B to a code L.  That may break efile or you may be able to force it through with the override.

If that doesn't work, go with IRonMaN's answer. 🙂