I'm so sorry to hear you lost all of your original flock, I can't begin to understand to heartache your family must be going through
Did you or your vet send a bird, tissue, swabs anything to your state lab for further testing to get confirmation on what illness you may be dealing with?
It's very hard to know what do to in these circumstances. You only have a few choices.
One that I would recommend to start is "sacrifice" one bird, send her for necropsy so you can hopefully at least get a "name" for the illness they are carriers of. This will give you more information so you can make the best decision moving forward.
You can also keep the birds, determine that you will keep a "closed flock" meaning you only bring in new birds - treat any birds that become symptomatic, but never sell, trade or give away hatching eggs, chicks, started pullets or show your birds. Any bird that lives on your property dies on your property.
A third option is to cull all. Clean, wait for a period of time, then start over. Knowing the disease you have helps in determining the waiting period.
I know these are generalizations and it's probably not what you want to hear. Each situation is different depending on what your chicken keeping goals are - not just short term, but long term as well - if you have even the slightest inclination that you want to breed or sell chicks in the future, then culling may be your best option.
As far as I know, you can eat the eggs of birds that have most respiratory illnesses as long as you following proper handling and cooking methods - just like you would any other eggs. Respiratory illness can affect the quality of eggs as well, sometimes shells make be weak or wrinkled or you may run into pale yolks or watery albumen.
The foul odor you are noticing from the 2 hens needs further investigation. Determine whether the odor is indeed caused by a sour crop issue or if it's from the disease. I am assuming you never detected an odor from your original flock, even when they were sick(?) Infectious Coryza is the only respiratory disease that I know of that reports a foul odor coming from birds - it is said they smell rotten. Sour crop should smell yeasty or like fermentation. If you suspect they do have sour crop consider treating them - I have linked the best article I know about treating crop issues down below.
Again, I am very sorry this has happened to you. If after all this, and you find that you and your family have hard feelings against these birds and you can't find pleasure in taking care of them, then it may be a kindness to cull them
http://www.backyardchickens.com/a/impacted-slow-and-sour-crops-prevention-and-treatments

Did you or your vet send a bird, tissue, swabs anything to your state lab for further testing to get confirmation on what illness you may be dealing with?
It's very hard to know what do to in these circumstances. You only have a few choices.
One that I would recommend to start is "sacrifice" one bird, send her for necropsy so you can hopefully at least get a "name" for the illness they are carriers of. This will give you more information so you can make the best decision moving forward.
You can also keep the birds, determine that you will keep a "closed flock" meaning you only bring in new birds - treat any birds that become symptomatic, but never sell, trade or give away hatching eggs, chicks, started pullets or show your birds. Any bird that lives on your property dies on your property.
A third option is to cull all. Clean, wait for a period of time, then start over. Knowing the disease you have helps in determining the waiting period.
I know these are generalizations and it's probably not what you want to hear. Each situation is different depending on what your chicken keeping goals are - not just short term, but long term as well - if you have even the slightest inclination that you want to breed or sell chicks in the future, then culling may be your best option.
As far as I know, you can eat the eggs of birds that have most respiratory illnesses as long as you following proper handling and cooking methods - just like you would any other eggs. Respiratory illness can affect the quality of eggs as well, sometimes shells make be weak or wrinkled or you may run into pale yolks or watery albumen.
The foul odor you are noticing from the 2 hens needs further investigation. Determine whether the odor is indeed caused by a sour crop issue or if it's from the disease. I am assuming you never detected an odor from your original flock, even when they were sick(?) Infectious Coryza is the only respiratory disease that I know of that reports a foul odor coming from birds - it is said they smell rotten. Sour crop should smell yeasty or like fermentation. If you suspect they do have sour crop consider treating them - I have linked the best article I know about treating crop issues down below.
Again, I am very sorry this has happened to you. If after all this, and you find that you and your family have hard feelings against these birds and you can't find pleasure in taking care of them, then it may be a kindness to cull them
http://www.backyardchickens.com/a/impacted-slow-and-sour-crops-prevention-and-treatments