There are some bacterial infections that will continue to be an issue for the life of the chicken/infected flock even after antibiotic treatment and apparent recovery. They will be carriers for life and will infect any new birds you bring in, it also passes vertically (from hen to chick thru egg.) Mycoplasma (MG, MS) is just one, there is also infectious bronchitis (IB,) infectious coryza, infectious laryngotracheitis (ILT,) Salmonella, and more. Stress triggers symptoms so adding or subtracting flock mates, moving coops, and any change in their daily activities can possibly trigger symptoms again.
There are a few options as far as treating and keeping a closed flock, or culling and starting over. If you have just a backyard flock for eggs it wouldn't really matter the route you choose. However if you have a breeding operation, it would be wise to cull and start over or you are going to infect someone else's flock, which is unethical IMO.
Something to note is that most of these infections also have an affect on egg production, your birds won't lay as well as an uninfected flock.