I had a velvet outbreak in Jan(didn't qt
new arrivals). Lost 3 fish in the proccess. I moved everyone to a 40 gallon qt
and treated with cupramine. I left the main fallow of fish (inverts are OK) for 8 weeks and everyone is back in and fine now. It was a nightmare, but pulled the rest through.
Many state that 4-6 weeks is enought, I did 8 to play in safe. Without fish hosts, the parasite goes through its life cycle and dies off. The fish may be clean right now, but because of the parasites life cycle, it may come back and attack 2 fold. Thats what happened in my tank, I waited too long. Its you call, but I would move them and get ready to treat. Make sure you have a proper copper test kit. I used cupramine and their test kit (seachem).
Here are a couple of articles
Maybe this will help you figure out what is is.