I certainly feel for both you and the breeder as it is very hard to hear of a litter where all the pups survived the birth process, whether natural or c-section, and then have pups lost. We have had c-sections here, and the pups were all fine.
My first thought, would be whether the pups were allowed to get chilled? It is extremely critical that pups are kept warm, particularly during the first weeks, as they are unable to control their internal temperatures. One reason why you want mom in with the pups as much as possible, is for being an on demand food source but also as a heat source. Breeders will supplement the heat with an overhead heat lamp and may also using a heating pad for extra ground level heat when mom is out of the whelping box when she's eating or airing. Puppy temperatures are a concern in the summer months, but even more so with a litter born during the winter months .... And particularly with the colder temperatures that we have all experienced this year.
As others mentioned, if the breeder had done all the health clearances, the mom was healthy before and throughout the pregnancy, the remaining pups continue to grow and remain healthy and the breeder provides a health guarantee, I would very likely pick my pup and start to train. If you are confident in and trust the breeder I would say stick with them. If not, there are many very good breedings out there with all the health clearances you are looking for.
NMH GMHR-IIII UH Dakota Creek's Royal Navigator MH (AKC & CKC) (NAHRA 500 pt club)
MHR Pine Acre's Dakota Sand Creek SH WCI
MHR-I UH Dakota Creek's Royal Gem
WR Dakota Creek's Wreaking Havoc SH
Dakota Creek's Cute As A Bug