Craftsman Pro Series tractor Kohler engine issue

Probably want be a problem but you replace cylinder you probably referring to cylinder head as the cylinders are part of the crankcase; therefore if one is bad both would get replaced.
 
But we could stand having the Kohler model and spec number so we would know what you have engine wise.
 
BTW I seldom ever do need to both cylinder heads on a twin cylinder engine. I do suspect that one of the heads is out tolerance warpage wise which is why they are looking at replacing it. Some Kohler engines use a thin all metal head gasket which can't seal well if the head is warped too much.