Are you using a tube to administer Baytril? If so, water is generally injected down the tube *after* meds to flush out any Baytril that may still be in the tube.

I agree with kellysballs; call your vet. It's very important to stick to the treatment plan exactly as you were told. Don't put us online peoples' advice above your vet's. Never change treatment plans without consulting your vet.

I'm guessing the water is just to keep your BP hydrated during a stressful time, especially if he's not eating. Again, I have not personally examined your snake, nor do I have a degree in animal medical care, so I can't tell you whether or not this is necessary. If you feel strongly about not doing this (trust me, I know how hard it is giving oral medication to an uncooperative snake!), give your vet a call and talk it over. Have this conversation with your vet, not us.