I have lots of 100% free range birds so I have issues like this all the time! I have to check my muscovy nests for chicken eggs. I've never had a chicken hatch duck eggs but I'm sure it will be just fine. She more than likely will stay on them the whole time and think they are her babies. I see no problem with leaving them alone, infact, it's what I would do. My husbands dad used to have these issues as well from what I'm told. He once had a duck hatch chickens and didn't think anything of it until the duck went to lead her babies to the pond. Yup, didn't end well! But since this is the other way around I can't see that being a problem.