This is VERY irritating! I ran into a problem myself when my orange hen, Rapunzel didn't like the black chicks she hatched out! They didn't have orange on them or look like the first two chicks.. I have no idea why really, but she started to peck them till they bled, so I removed them and brought in a foster mom, who was white, but took to the chicks immediately.
This is what happened to me. I put both moms in the coop outside with their babies, at first my white hen decided she needed to attack the other mom, and kill its chicks. I finally got them to a point where one stayed in the hen house, and the other in the run, and I just brought them all in at night. But occasionally something strange would happen, and they would start fighting or attacking eachother again. So I just took moms away. The babies wailed, until I took both moms in the house in pet carriers for the night (the chicks had a heat lamp). The next day, chicks don't care if there is a mom or not. After all, the moms are mostly there for warmth. But my chicks were so calm with the moms.. it was hard for me to let it come to that! But another problem you might run into is if you didn't vaccinated your babies for Mereks disease after they hatched!! They can get it from mom even if she is vaccinated, and its highly contagious!!!
But the chicks got along well, and have now developed their own pecking order. Except I hadn't vaccinated them for mereks thinking, cause my other chickens are so healthy, and because moms are vaccinated, my chicks should be fine. Well thats not the case. I just had to put one to sleep yesterday. Look up mereks disease. its horrible.
And I also had to do this with a batch of younger silkies I added to my older chicks a year ago. All I did was put the silkies in a cat carrier, let them get used to eachother. Then I let them in the coop, and watched them like a hawk. The first 24 hours is the worst! If they start getting mean, take them out only when they are going for the kill. It took me one day to introduce my chickens and they were of diff. ages so your chicks should be just fine. Its the moms and the babies that are not okay! Why should she be made to take care of offspring that doesn't smell like her? or are from her eggs she hatched? I'm pretty sure they want their genes to thrive, not another hens genes! They can instantly kill a chick they do not like or want! I hope this helped a little... and good luck with your chickens!