Baytril (or enrofloxacin) is one of those antibiotics where safety concerns have been extroplated from human medicine, without adequate studies in animals. No one that I know of has ever had a problem with it, but there are "concerns." If the disease process for which Baytril is being used is more dangerous than the supposed risks, then it is reasonable (but up to you) to decide whether or not to use it. Here is one reference, taken from a site for elephants, but citing the most commonly used formulary in small animal medicine (Plumb): http://www.elephantcare.org/Drugs/enroflox.htm
(I'll post some more information shortly)
"Contraindications/Precautions/Reproductive Safety - Enrofloxacin is contraindicated in small and medium breed dogs from 2 months to 8 months of age. Bubble-like changes in articular cartilage have been noted when the drug was given at 2-5 times recommend doses for 30 days, although clinical symptoms have only been seen at the 5X dose. Large and giant breed dogs may be in the rapid-growth phase for periods longer than 8 months of age, so longer than 8 months may be necessary to avoid cartilage damage. Quinolones are also contraindicated in patients hypersensitive to them.
Because ciprofloxacin has occasionally been reported to cause crystalluria, animals should not be allowed to become dehydrated during therapy with either ciprofloxacin or enrofloxacin. In humans, ciprofloxacin has been associated with CNS stimulation and should be used with caution in patients with seizure disorders. Patients with severe renal or hepatic impairment may require dosage adjustments to prevent drug accumulation.
The safety of enrofloxacin in pregnant dogs has been investigated. Breeding, pregnant and lactating dogs receiving up to 15 mg/kg day demonstrated no treatement related effects. However, because of the risks of cartilage abnormalities in young animals, the fluoroquinolones are not generally recommended to be used during pregnancy unless the benefits of therapy clearly outweigh the risks. Limited studies in male dogs at various dosages have indicated no effects on male breeding performance. Safety in breeding, pregnant, or lactating cats has not been established."