That helps to know she has laid eggs. What age did she start laying? Has she laid several times or just once? What many owners do not realize is that captive raised birds will breed at too young of an age. One theory is they mature more quickly. However, young pairs do not have a good track record, and females have the added risk of egg binding, which seems more likely if she is too young. Most likely wild parrots simply do not bond with a mate as early as we pair them, and that is why they breed at an older age. Also, people who breed birds for shows – like showing dogs – will not let their birds breed at a young age. For example cockatiel breeders for show do not start their pairs until they are between 2-3 years old. But most captive cockatiels can lay eggs as young as 8 months. Therefore, I always advise a breeding age that the wild counterparts begin breeding, and with smaller conures that would be 3-4 years old, and larger conures, 4-5 years old. I realize I assumed you have Green Cheeks since that is what most people seem to have these days.
Depending on what age she first laid eggs, and how often she has laid, this can have an effect on what is going on. She may just be tired and not receptive, and this definitely can cause mate aggression. If these are a larger conure species, they are probably too young and this may be what is going on. Either way, it sounds like they aren’t in sync right now, so give him a chance to cool off and then they should get back to where they were. Regardless of species, I recommend a 6 month rest between each clutch, whether the eggs hatch or not. Forming and laying the eggs is what takes a toll on the hen’s health, so she needs that time to build up her resources and recover from the physical strain of egg laying.
Thanks for the update,