[souffle]

That is a shame. I hope you now realise that you must never keep hamsters over 4 weeks together as they can and will mate with each other. The older pup likely had something wrong which was sadly why it was lost. It is common for them to die at this age due to being able to make the full transition to weaning if there is an internal bowel problem.
There would be a reason for Ellie to cull the litter. Number one reason is stress due to interferance from the owner. They must be left absolutely alone and just visited for food and water. We would never know how many pups a female has until they all have eyes open at 14-17 days when we would start handling them.
The second reason would be that mother detected something was wrong with the pups. This could be a genetic fault due to mating with her brother. Mother always knows best and we must respect her decision. They can detect things wrong inside pups and will cull them because they know that is right.
Another reason is that the mother is ill herself of has no milk. This happens with young mothers often. If they get mastitits (sore teats) it is painful for the pups to suckle and the milk is tainted and the pups may die. It is natural for a mother to dispose of dead pups by eating them.
Are you sure she has no pups left in the nest? Staying in there is a sign that there may be some left but also the symptoms are those of a hamster who is not feeling so well. If her behaviour is odd it is more likely she is not well and in this case I would feel I had to check the female for problems. You need to look for signs of and discharge from the vents, diaorrhoea, messy underneath, swollen belly, red or swollen teats and using a clean spoon rubbed in the bedding check the nest of any pups dead or alive. Dead ones should be removed with the spoon. If there are definitly none then clean out the whole cage and see a vet if there are any problems with mum. The cage clean will help her forget about the pup. Some mums do fret a bit but this should pass in 5-10 days or so.
Don't ever put her with any males again will you. It would be too much strain for her.
Sorry you lost the pups but hope mum recovers well now.