Hi Lolly,
In general Herxheimer or 'die-off' reactions tend to exacerbate existing symptoms or frequently people experience something akin to a flu-like illness with general malaise, fatigue, headaches and other aches and pains. If you consider that killing Candida / yeast and other microbes releases extra toxins into the bloodstream and triggers an unavoidable immune response then this makes sense.
In some cases people do report new symptoms during die-off reactions based on the many reports I've read here on this website and others, as well as in books and the few research papers on the subject.
Did your daughter already suffer from loose stools as a symptom of her illness? Could this just be a worsening of this? If not it could just be that any dead yeast cells and their contents are irritating her gut lining and thus resulting in looser stools. If this has happened with other anti-fungal supplements or medications it might confirm this - or perhaps Candigest is just doing a better job resulting in more of the above irritants in her gut.
If it were me I'd do as you plan, stop the Candigest and see if things improve. If they do you have your answer and maybe a lower dose or alternative anti-fungal may be worth trying - ideally with the supervision of a doctor or nutritionist. Is your daughter seeing anyone about her condition?