Managing a hive for excess honey means also understanding the flow, brood timing, and other factors.
Your way past your main flow. So if you left on supers all summer, and perhaps allowed them to have an unlimited brood chamber, then of course they will eat back half (if not more) of what they stored. Do you have Italians that also seem to never shut down in a dearth? Your main flow was probably over by the end of June. While they may still have nectar coming in through July and Aug, it usually amounts to nothing in gaining stores.
Take your honey off by the end of June. Compress the bees back down to their wintering configuration. By doing so, they will stop brood production and many times be in a better position to harvest honey and yet allow the bees to not eat all their stores by raising brood all summer in times of little nectar flow.
This year, there was a nice long clover and nectar flow after the cold rainy spring.
Management of your bees is much more than putting on supers, leaving them on all summer, then expecting a huge surplus.
Collector your surplus in June and then putting back wet supers also stimulates the hive to keep collecting. As it is, your bees probably stopped collecting from any main flow weeks ago, but probably kept raising brood.
You have to remember that in nature, the bees will quickly fill the brood area in spring (And why they swarm), limiting the queen and having much less bees being raised all summer long. We as beekeepers usually never allow the bees to be effected by limited space (by constant supering), and the queen never shuts down. So what we do as management, not always gets us the results we want.
Understand what bees do in nature, what they are inclined to do, and understand your part.