Sometimes when a storm dumps a lot of water in a short period of time, even normally sound areas can become flooded. If the ground is dry it could be a temporary problem with absorption. I wouldn't worry too much but it's something to keep an eye on.
I would still keep them within sight but separated for a couple of weeks, after you've sorted out the separate enclosure for weatherproofing. After that you should be fine to introduce the young ones into the main flock. They are old enough now.
The chicks were afraid because they've probably...