Thanks for the additional information. It is helpful.
There are many reasons your puppies may be dying that include serious worm infestation, flea infestation causing anemia, herpes virus, and bad milk from mom or congenital health issues. It is sometimes referred to as fading puppy syndrome.
This site has information on fading puppy syndrome.
You can read about herpes here:
This site goes over ways of helping save fading puppies.
Normally I would suggest you have at least one pup checked by your vet to help determine a cause. If mom is inexperienced then you can't use her as an accurage judge of the pup's viability. An experienced mom will often not feed a pup that has problems or is ill. Herpes could be playing a roll in the passing of your pups and if this is the cause, she shouldn't have a problem later.
Unless your female was dewormed in the last couple of weeks of her pregnancy, she likely passed worms to the pups which can lead to a weaked state but I wouldn't expect them to expire this fast. A fleas infestation can lead to death but if she is on flea preventative, that shouldn't be an issue either.
Now the whelping area should be around 90-95F the first week, and 85-90F the second and then 80-65F the 3rd week. After the third week, a puppy can maintain their own body temperature. A heating pad is helpful but only if a portion of the whelping area has the heating pad and the other a covering that will allow the pups to move off of the pad when it gets too hot and not be on a cold surface.. If they become chilled, they develop an upper respiratory infection and go downhill very quickly. Sometimes a heating pad will help dry up fluid in the lungs but often a pup won't make it once they become chilled. The same applies to aspirated formula. If a pup is not swallowing correctly, formula can be aspirated into the lungs leading to aspiration phneumonia. This happens quite often with bottle fed pups since it can be quite difficult to get the right about of formula. In fact often breeders will use a new makeup spong to deliver formula to newborn pups being careful to inspect it often to ensure no pieces become loose and are ingested accidentally. The sponge helps minimize aspiration pneumonia.
Being too hot from laying too long on a heating pad can lead to dehydration especially if they are not eating well. Dehydration kills fairly quickly. I'd be inclined to have the one that is now slowing down seen by your vet to determine if herpes is the cause in his opinion especially since you do still have a week or so before the other pup can regulate their own body temperature.
If it is herpes at least it won't be an issue with her next litter. If it isn't, then you do have to determine if the cause is congenital, or environmental or parasitic. If congenital, you will not want to repeat that particular breeding. If environmental, you will be better equipped to handle the next litter and have a suitable draft free area for the whelping that can be kept at an elevated temperature for a few weeks. I know my electric bills is always much higher after we have a litter.
You might keep in mind for future litters that adding a drop of pancake or karo syrup to the formula often keeps a pup interested in nursing. A smear on the nipple often gets a strong suckle going as well. I would seriously consider having the fading pup seen as soon as possible.
I hope this information is helpful to you. If you would like any additional information or have more questions please don’t hesitate to press the reply to expert or continue conversation button so I can address any issues you still have . If you do find this helpful, please take this opportunity to rate my answer positively so I am compensated for my time.