I don't have a cover on the fluval intake, but my husband is a master at cutting and carving sponges to cover them, that's how I cover my filters in all other tanks so the shrimp don't explore too much (lol).
Great, get hubby to make a filter intake cover and you'll be fine. After they hatch, they won't move around too much, they'll absorb their eggs sacks so it'll be close to a week after hatching before they'll go looking for food.
Please leave the BN eggs alone. They are not like other eggs that are deposited singly. They are all attached as a mass. The infertile ones will not harm the ones that will be hatching. Dad takes care of it all! He will start to eat the infertile ones away.
Hopefully the new hatches are ok. So close to hatching is a very fragile time for those fry. Fiddling around with the egg mass can force some of them to hatch too quickly. Good luck with the babies and pics when you can!