Welcome to TBN. You probably would get more help with a little more information and a few pictures. Are you talking about the PTO shaft?
Don’t remember seeing anyone crack a housing removing a PTO shaft but seen plenty crack from have too long of a shaft on an implement. The damage occurs when they lift the implement with the 3pt hitch.
The rear case cover on my M9's is removable and replaceable but it's not cheap. You might find one at a tractor salvage yard. Not sure about yours but I presume it is.