Yes, the 6 week old kits will need to be weaned and separated from mom. I wouldn't let them nurse from the other doe(especially don't put them in with her as she could attack them), I would just wean them. If possible, the best and least stressful way to do this for the kits is to move mom(and her nest box with new kits) to a new cage/pen, and keep the 6 week old kits in their usual cage/pen until 8 weeks and they go to their new homes, or at 10-12 weeks separating them into their own cages/pens.
To best protect their digestive function so weaning enteritis doesn't occur, I wouldn't be giving them any new foods or treats, and would continue with their same brand/type of pellet(as long as it's not causing any major health issues) and would free feed a good quality(no mold, no noxious weeds) grass hay, and making sure they are eating their hay and pellets really well. And keep a very close eye on their bums for any signs of mushy or runny poop. Watery diarrhea or mucous in the poop would be an emergency, but mushy cecotropes with normal fecal poop is usually not an immediate emergency but indicates a need for a diet change(more fiber/hay, less starches/pellets).