Missing vaccines

My husband took our 11 month old to the health department the other day to get his missing shots. When I called His doctor office back in February they said the next availability they had for him to get his 6 month well check is in November when he will be one. That alone is ridiculous. When my husband picked up his shot record from the doctor to take with him they had that they had not given him any shots.... Ever! I specifically remember my baby being very miserable for a whole day from them giving him quite a few shots in his thighs when he was about 2 months old and again at 4 months. The health department said since there is no record of this, they would have to give him all of his shots again. Can't that hurt him?