Yes it will harm the ferret you must change the food everyday same with the water it important expecially with the warm weather the litter needs to be changed every 2-3 times a week.

 If you are finding fly larva it may be the food you are feeding it try and get a new bag of food. Sometimes flys get picked up from the company that is supplying the food. I'd contact the company that the food is made by. And yes it is dangerous for your ferrets because fly's carry a lot of diseases, you don't want maggots to form in the digestion area or else where in your ferrets. If you keep the food dish outside of course fly's will get to it when ever and where ever fly's land they leave larva. Try keeping the dish inside or in an area that it isn't open to bugs getting to.