Awww, I hope Isabelle is feeling better by now!
It's possible that it could be an allergy or sensitivity coming to light. But it also sounds similar to what happened to Christopher early this year. All four of us had terrible, terrible nausea, vomiting and diarrhea in late February. The worst of it lasted for a couple days, but none of us felt 100% for at least a week. Christopher, however, had it the worst. He had the initial day or two of vomiting, then a day off, then he started up again with the vomiting and I couldn't keep him hydrated (he WOULDN'T drink anything). On the advice of his pedi, he was admitted overnight to the hospital and seemed to be better, but then he would have episodes of breakthrough vomiting every now and then. This lasted a few days, but gradually became less and less with each day. It was exhausting, to say the least. His pediatrician did tell me that it was pretty common to happen though.
I'm hoping that Isabelle had nothing more serious than that! Update us if you can.