Is there a concern for the potential of future congenital malformations in offspring when preservation of eggs and sperm is done AFTER cyclophosphamide treatment given that it is an alkylating agent?  

No, there is not a significant risk of congenital malformations in embryos created with cryopreserved gametes or unassisted pregnancies AFTER cyclophosphamide use. While alkylating agents lead to both male and female infertility, congenital malformations from cyclophosphamide occur when conception ...