The grating sound emanates from the knee cap joint. A sizeable proportion of patients who have undergone ACL reconstruction with the patellar tendon (BTB) develop patello femoral pain and crepitus. You are lucky if you don't have pain. Again a sizeable portion of the normal population also develop arthritis in the same patello femoral joint from mal alignment related overload, age etc.
This again settles down with the right kind of exercises. You should have a balance of stretching, isotonic exercises and avoid overdoing them.
The sound may decrease as muscles build up due to perhaps a rebalancing of the muscles but may not be abolished given that arthrosis has probably developed under the knee cap. You need not stop them.