You're missing the point. A higher number of chromosomes makes it easier to do targeted selective breeding because it's less likely that a desirable characteristic will be on the same chromosome as an undesirable characteristic.
But linkage is a function of distance from one gene to another, so all you really care about is whether your desirable gene is physically close to your undesirable one. Having things broken up into many chromosomes helps only a little bit, if the break happens to be between the good and bad genes.
During reproduction, chromosomes are "mixed" together [1]. You don't get a straight copy of the parent chromosome.