In my experience muscovies are very easy to breed - they need little encouragement. Access to swimming water is always a plus, adequate feed and a safe environment in which to lay and brood their eggs. They are excellent at brooding and protecting ducklings.
Allowing her to build a full clutch by leaving the eggs might encourage her to go broody. I never removed eggs from my hens. If you only have the one hen, she may be somewhat over mated. Drakes are horny creatures. Some drakes will even try to breed hens while they are setting on the nest.
Actually it only takes 3 days from an initial mating for eggs to be fertile. Chickens can maintain high fertility for two weeks, moderate fertility for three weeks and some fertility for up to a month after mating. Not certain about ducks, but they can retain viable sperm for considerable time also.