I'm so sorry to hear this, the tiny new kittens will have very little immunity especially if their mothers are feral also. Heart-breaking news. I hope the shelter can get over this set-back. If at all possible, it is important to get the yearly inflenza injection for our cats. I know the local vets do what they can, what about a rota of local vets to visit the shelter when required and innoculate any new kittens that arrive.