After the flight to the ISS yesterday I am reading more stuff about mankind in the universe.
In general, those kinds of balloons cannot be reused. There was a concern, I don't know if it was a Manhigh flight, where one balloon had burst when strong winds bounced it on the ground, and the spare was used on another day. But the weather was iffy, and if that flight had to be scrubbed they couldn't reuse it once they had started inflating it, and they didn't have another on hand, so that could have delayed the entire project. Used balloons were sometimes given to farmers, who used them to cover hay. I don't know specifically what happened to the Excelsior balloons, but I presume they made it to the ground since the gondola was recovered and reused. Ground control could operate the valves in addition to receiving data, and they had a man on the team who could predict the landing site. But there is no reason they would have kept them.
If you want to read about that in more detail, you might look for the book The Pre-Astronauts: Manned Ballooning on the Threshold of Space, by Craig Ryan.