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Dear Andrew,
The symptoms you describe could be caused by a yeast (candida) or a viral infection. Both can not be treated with antibiotics. Candida especially can occur when antibiotics are given. Enrofloxacine itself normally doesn't give side effects with the dosage you describe.
It is not always absolutely necessary to treat with antibiotics before vaccination, only when there is really a diagnosis and/or a strong suspicion for paratyphoid. In your case I would just vaccinate the birds without any other treatment. Be well aware, though, that the birds are completely healthy at the moment of inoculation.
Kind regards