There are several layers of cartilage in the knee. The C-shaped meniscus between the bones is the most commonly known. But your son has damage to the next layer down: the articular cartilage. This is a more pliable, softer cartilage that lines the inside of the joint. It’s between the meniscus and the bone.
Repairing damage to the articular cartilage is a little more complicated than stitching the meniscus back in place. With defects or holes in the cartilage, it’s more a matter of plugging them up and smoothing them over, then letting nature take its course.
The type of surgery you mentioned is called osteochondral autograft transplantation (OAT). The surgeon does, indeed, harvest plugs of good, healthy chondrocytes (cartilage cells). These are taken from a part of the knee joint that doesn’t get used much (non weight-bearing site). The plug (or several plugs) are then used to repair the lesion.
The technique works fairly well (especially in young athletes) but there is some question about durability. Long-term studies just aren’t available yet. The outcomes after two years seem positive. But there are some failures and the reasons for these failures have not been determined.
Studies are ongoing to investigate the results of cartilage repair. Clearly more studies are needed to find out what happens in the long-run and how durable this type of repair really is.