In all honesty, I NEVER use medicated feed. I keep the brooder clean, and have never had problems. On the rare occassions that any of my birds get a bit of runny poop, I add a generous amount of ground hot peppers to their water (Cayenne works, I grow thai hot peppers and keep a bag of dry on hand). The birds don't notice it, poop clears up.
You need to keep them on it for awhile still. My medicated feed says you can keep feeding it all the way up until they starting laying, which might be a little excessive. I would just go ahead and use up what you have. The medicated feed helps to prevent/build and immunity to cocci. that your chicks can get from the dirt. It does not matter how clean you keep your brooder. It comes from outside. Even if they have not been outside yet, they will eventually go outside. Keeping them on it certainly won't hurt them. It can only help!