They likely will if your birds are still sick.So, my gut tells you that you are right about this. That they were carrying the disease and then the stress of transport made it active. So my question is this, if I get chicks from elsewhere, will they just catch it from mine and it’s pretty much hopeless?
You are supposed to quarantine new birds as long as possible, as far from your birds as possible. Even if your birds are cured, not quarantining can introduce another pathogen to your flock. Some people haven'd taken the precaution and continue to introduce disease and it becomes a vicious cycle.
Ideally quarantine should be 40 days and at least 50' from your flock. Then deal with your birds first and then the new birds, changing shoes and washing up between and after. I realize many don't have the means to separate that far but know that some pathogens can travel 1/4 mile or more through the air.
Unless you know the specific disease, no one can answer that. Birds will be lifelong carriers of some viruses and bacteria, others not.I definitely will. But will my current birds (if they live) be carriers for life and always infect new birds?