I'm sorry about your troubles.
What organism caused the respiratory disease? Without a definitive answer to that question, most people assume it is MG/MS (Mycoplasm gallisepticum/Mycoplasm synoviae) or some other contagious disease. And yes, they will be carriers for life. MG/MS can be spread through hatching eggs so selling hatching eggs/offspring from infected birds can infect flocks of those you sell them to - something I am sure you do not want to risk. Without ruling out MG/MS it would be highly irresponsible to sell eggs or offspring.
In this state (KY) and many others, a diagnosis of MG/MS is a death sentence for all the birds on the farm (or lifetime quarantine for the farm). It is a reportable disease and spreads rapidly. Carriers can appear healthy for long periods of time, only becoming sick during times of stress. Since you ask about adding them back to the flock, I assume that your other birds were exposed to the new birds at some point. It is possible that all your birds have been exposed now.
You have a couple of options. You can assume your birds are infected and keep a closed flock, letting no birds or hatching eggs leave your property. Or, if you want to be sure, call your local Dept. of Ag and inquire about having your birds tested to rule it out. If you decide to have them tested, just know that a "positive" will likely mean depopulation of the birds on your farm. Since MG/MS does not live long without a host, after sanitizing everything, you could begin to repopulate after about a month.
As for sterilizing the quarantine area, clean out thoroughly using Oxine (recommended) or bleach solution. Your local Ag dept may have other suggestions.
Good luck and keep us posted.