This is the way the transformation from AA to hypoplastic MDS was explained to me...
The hematopoietic (or blood-producing) stem cell differentiates to another type of stem cell that further differentiates into the lymphoid progenitor cells (that differentiates to make all the different types of WBCs) and myeloid progenitor cells (which differentiate to eventually become the RBCs and platelets).
If an immune attack is going on, as in aplastic anemia, most of the blood cells will be killed off in the marrow. If the attack continues the progenitor cells further up the line can also be damaged. If this happens, they start to make dysplastic cells. If it happens to enough of the progenitor cells upstream, then the marrow starts to look more like MDS then AA.
One thing that makes the differentiation so hard between AA and MDS is that the marrow is fluid. So, what you see during one BMB aspiration may not be the same thing that you see at your next. For me, I had some BMB's where I was hypocellular and others that were hypercellular.
I don't think this line of thinking necessarily applies to AA that transforms to MDS 5 years after IST, but it does seem to make sense for the initial diagnosis if it is immune mediated.
52 yo female, dx 9/08, AA/hypo-MDS, subclinical PNH, ATG/CsA 12/08, partial response. Tried slow cyclosporine taper over 4+ years. Platelets fell, so back on cyclosporine. Trisomy 6 clone in 5% of cells.