Sometimes it does, due to the (near) total ignorance of what this is all about.
10 years ago I was briefly employed by a contractor for a state government that was working on a system a bit like this, although not hardly so life critical. The original system had been written and customized by the one of the big names like Lockheed or CSC and was pretty good as these things go ... but the state put continued maintenance out for bid and gave it to another company. With no transition, and really counterproductive budgeting.
I.e. around a year previously another guy was hired to do what I did, and let go after a month or two because of money.
What was I hired to do? The most difficult job of software archaeology I've ever attempted, not counting one code base that was impossible (https://news.ycombinator.com/item?id=6092960). The original programmers, probably on site, used SCCS (!) ... until they stopped some months before producing the binaries running on the system.
Other minor details: the system ran on DEC Alpha hardware and their version of UNIX(TM), and of course by then it was a doomed system with no migration path for binaries. The state budgeted the project and made its milestones based on estimates made by another consulting company, and those were not based on reality.
I bailed when it became clear there was no possible way to meet the state's demands, e.g. a point when I realized that if there was a way to recreate the production binaries I wasn't going to be able to find it, and they were assuming the sources were in a lot better shape.