That's when you have to manually input the new price and override it with the override card. That's what happens to us as well. Pain in the a$$ for us too. Youd think they would fix it. Sometimes it dont work, and kicks out the altered price even with an override. So what we did was just give the item for free. 

To accomplish this, we wrote down the plus code during scanning, give the item of the override didnt take, then have icc scan thebitem.out as "damaged." 

Corporate got curious as to why and we explained the coupon system.was busted, so we had to do this.