I posted a while back for suggestions to help Shamrock stop being
aggressive to Bonnie. Bonnie is the former feral who imprinted on
Shamrock; Shamrock adored her. After Shadow died, and I got the 2
kitten littermates, Shamrock bonded with them and turned his
aggression on Bonnie in the same way he acted with Shadow. I
wouldn't have interfered, but Bonnie was clearly stressed and she
hid under the bed a lot. It's been a few weeks now, but I started
putting Shamrock downstairs during the day and leaving the kittens
with Bonnie upstairs. This has been difficult in the food
department, but it's worked out well for peace. Bonnie has bonded
with the kittens and has gained confidence and plays
with/chases/gets chased with them. Shamrock still chases her, but
she doesn't act nearly as afraid, and Shamrock doesn't seem to act
like he's being punished. I give him lots of attention when I get
home, and he sleeps with me and the others don't.

I think there is a lot more "conditioning" that has to happen, and
this is a long process, but I think it's helping. My initial hope
was that Shamrock would play with the kittens when I'm home because
he couldn't all day being separated, leaving Bonnie alone. He still
tends to look at her funny and the kittens aren't nearly as close
to him as they were, and he'll launch a chase attack around the
house with Bonnie as the target, but it isn't as intense as it was
after Shadow died and the kittens entered the picture. I don't know
yet if this is the right thing. Oh, they (Shamrock and kittens) are
still close, but Shamrock doesn't hover over them and clean them
and protect them like he did.