Thank you so much everyone for the replies. Just as a quick update, she's doing much better. She wasn't eating for 2 days and then just went right back to normal. I noticed the biggest difference after bringing her in for a warm bath. I ended up getting rooster booster and adding it to their water(and will continue to do so) and also bought some VetRx after a friend with a sick Muscovy had recommended it. I only ended up using it once and after that she was already doing so much better. She's now back to 100% her old self.
I still don't understand what happend to cause all that, but it definitely made me think more about having things ready for first-aid. I got packets of electrolytes to keep on hand and now I have the VetRx. I need to get some thing for cleaning wounds too, just in case. Any other suggestions for things to keep around would be great. A stethoscope is a great idea, so I might track one down. Hadn't ever considered it before.
And to answer the previous question, yes, they have water at all times. I just think they were eating too fast for a while there. I started moistening their food every morning to help and they've since calmed down during feeding time.