Good for you getting her seen and getting her meds
You should not give the antibiotics in water. Did you get a little syringe and what is the name of the meds? Normally it is Baytril and the dose is 0.1ml once a day. Phone the vet and ask if you can give her the meds straight in to her mouth. Baytril tastes horrid and a hamster will avoid drinking. They never get a proper measured dose in the water if they get any at all. To give the meds you need to get a little cloth and wrap her up so just head pokes out. One person holds the swaddled ham and the other puts the syringe in the side of the mouth and squirts the meds in to the cheek. She will not like it but quickly give her a treat to wash it down.
I really would encourage you to try and give her it this way as she definitly will not get the meds in the water.
I think she is stressed out by her visit which is why she is unsettled. Try putting her in a dark quiet room and hopefully she should settle down again. Hope she is better soon.