One of the big reasons why allogenic bone marrow transplant works. The recipient gets chemo and radiation to kill off all of their own stem cells, which are mostly cancerous by this time. Not all die off and some may survive to cause a relapse of the leukemia.

Even in a 10/10 mhc match, the donor cells can't be perfectly matched to everything, so some graft vs host action is thought to be the Final element in battling whatever cancer cells may remain. To check for residual leukemia cells, they often look at the bone marrow for chimera - % of graft vs pretransplant stem cells....

Hope that answers your question