In cases where unions are involved, the terms of the furloughs are usually negotiated with the unions beforehand. I don't know about contractors specifically, but for civil servants, their unions were definitely involved in the furlough negotiations during sequestration. In this case I don't know how much they'd get to say since the entire federal government has shut down and the issues go all the way to the highest parts of the government.

Also keep in mind furloughs are not layoffs - just unpaid leave.