Hello,
This sounds like a allergic reaction to flea bites or fly bites which is fairly common in dogs. With the medication he is on I would suspect this will take around a week to clear up and heal. You will need to keep the area clean as well and continue using the cone to keep him from scratching.
Once this has cleared up you will want to monitor the area in the future to make sure there are no more bites that get infected again.
Walter
Breeder
Breeder and pet health consultant. Have spent a number of years with dog rescue, training and health