I infer you mean the gift coupon code only discounts the original item price, rather than the current item price, leaving some remainder to be paid? Discount Codes retain whatever discount value you'd set them up with, so when you updated your item price, you may have needed to update all your Discount Codes for those gift coupons accordingly.
There's one way to avoid that necessity to "future-proof" discount codes, if they're Item Unit Price discounts (rather than Cart Item Total discounts). Item Unit Price % Off discounts can't be set to 100% for technical reasons, but you can set the Discount Amount as a Flat Amount in excess of the actual item price, higher than you'd ever expect to sell the item for. When a buyer applies an Item Unit Price discount code that's valued higher than the actual item price, that just discounts the item price to zero.
If you have a huge batch of discounts to amend that would be too tedious to update one by one, we may be able to help facilitate that if you email support about it:
