How to keep track of hatchlings
Are they supposed to hatch at the same time? If not leg bands might work well but if so I think you'll either need to be there when they're hatching to manually separate them. I've heard of dying chicks by poking a hole in the shell, injecting dye and sealing it back up but I think it's really risky because you can introduce bacteria too easily and I'm not really sure how humane it is.
You probably already have, but pencil marking the eggs so you don't forget which batch they're from would be helpful. I suppose just before hatching you could put a a barrier make of card stock or something to keep the two batched from mixing. Then it'd be pretty easy to give them colored leg bands that indicate the batch. Just make sure they're the right size! And as their leggs get bigger you want to make sure the band never gets tight.
Maybe a more experienced person has a better idea?
Would not wear off any faster than them replacing their feathers I would think. I assume it would permanently dye whatever it touches. The issue I am now thinking about is color though. Red is bad since birds often peck at it thinking it is a wound. So whatever you do, go with a green or blue or something not close to red.
Small zip ties come in a few different colors and when they grow bigger you can cut the small off and add a bigger size,and just cut any excess off.You will need to handle them when they go into a bigger pen so do all your needs then.Like trimming toes nails,beaks dusting and changing bands,you don't want to handle them any more them neded..Don't forget to write down what bird gets what band.