Hatching from Mareks positive flock

The vaccine is not an effective treatment. It only acts as something to hide symptoms. Personally, I would not hatch eggs from sick birds.
Here is a paragraph from Penn State University article-

"So how can you prevent Marek's Disease in your flock? Vaccination of day old baby chicks is the most dependable way to prevent the clinical disease. Birds must get the vaccine before they are exposed to the virus. Then the birds need about 4-7 days for the vaccine to do its work. That means complete isolation of the chicks for at least this time. The chicks should be kept away from other birds and have a separate caretaker for them. If a separate caretaker is not possible, the chicks should be cared for first before caring for the others. Caretakers should shower and change clothes if needed to go back and forth between age groups. Again, this is for at least 4 days. "

It's important to note that the virus is transmitted via dander. Though chicks hatched, vaccinated and reared for a week by a different care provider isolated from infected flock will be immune...

I was about to be long winded in saying the flock still needs to be closed and isolated. Even the birds with the vaccine. There is no effective way to rid uninfected birds of the infected birds dander. In the words of Bonnie Tyler it's "living in a powder keg giving off sparks!"- an explosive situation.

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