I can't provide any real knowledge but I typically keep the stock very simple--just vinegar, celery, and bay leaf. After it's done and cooled I'll make a proper vegetable and herb soup. The flavor is definitely better after a day so I make a pot in advance and heat up 1 bowl at a time.
Minerals are durable, but the other plant compounds seem to be delicate and vanish with time/heat/light/etc. so I'd probably peel and grate the roots later as part of the soup recipe. Wikipedia will often discuss the toxicity threshold of specific foods.