You need to see a vet with her and take her and the litter (if there are any babies) with you. It sounds to me as if she has an overwhelming infection and if you lose her you lose the entire lot as these pups will not survive without their mother. If she has mastitis or a womb infection she will be unable to feed the pups and handrearing pups this age is practically impossible.
The mother is your priority and no vitamins nor veggies will help her. She needs vet attention quickly. This is not normal behavior for a female with pups especially if she was sickly beforehand.
Is there a bad smell around the nest?
Another issue is the cotton bedding. This may be the cause of the problem. It is very dangerous as hamsters when pouching it swallow some and it can block the bowel. If she has a bowel blockage she will need given rest. I don't think you can remove this right now if you have live pups in there so get her to a vet.
It's not a Romeo and Juliet situation. It's instinct for the male to seek out a mate and allowing him access to the female is really a bit of a disaster especially given the fact you did not know the genetics of the parents and one is a white who could be carrying the eyeless white gene
Make sure your cages are very secure and this can never happen again.
The blanket over the cage will be fine to give her privacy for now as long as you ensure there is ventilation. If there is a bad smell you must check using a clean spoon for dead pups. If mother is not constantly in the nest they are likely dead I'm afraid but again see a vet asap.
You should not self prescribe medication in case it is the wrong type. Pet shop meds are no use. Did you see a vet for the medications and what did they say?
Please let us know how things turn out and sorry for the bluntness of this post. I hope she rallies round for you.