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Have a flag on the transform to remove empty fields.
One could have a map with 2 fields
F1->Mapped to DataField DF1
F2->Mapped to Data Field DF2
If the data doesn't have DF2, there should be a provision on the transform to say remove this field
So the output when there is no DF2 field should only be F1->DF1 and the empty F2 which did not receive a value from DF2 should be removed.