Well, they have only had 3 days of antibiotics, right? Are they drinking enough of the medicated water? We don’t know what the name or the dosage of the medicine is to help with that. If the chicks have bronchitis, they may be sick for a few weeks to a month. It they have MG, they may get better in a few days. Sick chicks can be chilled and need extra heat.
Coryza smells rotten and usually causes thick nasal discharge and pus in the eyes. They are more sick than with MG or IB. There is no way of knowing what they have without testing. I have only dealt with bronchitis in my flock, and it did seem worse at night, just like when humans have a cold virus. So I would make sure the chicks are drinking well, and put some of the medicated water in a small bowl of their food, in case they will take more that way.
You cannot really disinfect a brooder, but just keep the bedding stirred and dry, and add new when needed. When it is really soiled, change it completely and use some Lysol or similar product on the bare floor. That is about the best you can do. Make aure they have good air circulation.