My first question is where you found out about the feeding schedule and whether it's really appropriate. If conures are anything like cockatiels, this baby needs more than two feedings a day right now based on his current stage of development. Is he gaining weight at a good rate?
There's a handfeeding schedule for cockatiels at
http://www.cockatiel.org/articles/handfeeding.html Two feedings a day is recommended for fledglings, but the age recommendations aren't appropriate for a conure chick because it takes them longer to reach fledging age.
The way to eliminate a feeding is to gradually taper off - feed a little less each time until you've reached an obvious stopping point. But the expectation is that the baby will make up for it by feeding himself, and you would provide easy to eat foods for him to experiment with. But babies usually don't start feeding themselves until they fledge, so if you eliminate a feeding sooner than that you have to watch carefully to make sure he's getting enough to eat. That's more important than following the schedule exactly.