If this does not help, and the diarrhea persists, have a longer exam by the vet including a complete blood count. Sometimes coccidia does not show up under the microscope but it can cause anemia because it causes hemorrhage. You need to replace fluids your chinchilla is losing. You might want to put some Pedilyte into the water for electrolytes. Weigh your animal daily.
Weight loss is dangerous.
Stay in close contact with your vet here, as this is probably a major problem. Return to the Etc.