That really sounds like a lot of work to do...usually if you just shut the air off for a few minutes on your hatch, the empty shells float, the live BBS will swim around the hatching container, and can be collected by using a light to the containers side, (2 liter soda bottle). If you wait a few more minutes, they start to settle to the bottom and can be removed there by a piece of air line or if you fitted the bottom of the bottle with a stop-cock valve.
Conversely, you could try decapsulating the cysts which is not hard to do and hatching... or better still, those juvenile corys should take rehydrated non-hatching Decapsulated brine shrimp cysts.(just soak the nonhatching decaps for 15 mins before feeding.)
hth,
al