Genotype of children conceived after stem cell transplant?
Spermatozoa are produced in a process called spermatogenesis. They come from germ cells, which in the human males are located in the testes. These are not affected by stem cell transplants. 

In females, the equivalent oocytes are already present at birth. They undergo meiosis later, but since their genetic composition is already set at birth, they, too, are not affected by stem cell transplants. 

This might make the process clearer: Primordial Germ Cells and Sex Determination in Mammals


  In all vertebrate embryos, certain cells are singled out early in development as progenitors of the gametes. These primordial germ cells migrate to the developing gonads, which will form the ovaries in females and the testes in males. After a period of mitotic proliferation, the primordial germ cells undergo meiosis and differentiate into mature gametes—either eggs or sperm


A stem cell / bone marrow transplant only affects the bone marrow, where the blood cells are produced.