How curious you are!
Yes, some parts of OS 9 have not changed much since System 7, but I think almost all of the OS code has at least gone through bug fixes and minor improvements. The problem with 9.1 is that all human resources at Apple have been busy building OS X for more than a year, and only a small group of developers still work on OS 9. The group is very small and the OS is very large and complicated, so these days they simply don't have enough heads and hands to re-write some components. Nevertheless, OS 9.1 is a large-scale remake of OS 9. They have widened almost every bottleneck, including the complete (according to some sources) re-write of the process manager in PowerPC-native form.
As for lost source code, I doubt this has ever happened to Apple's developers. I presume the problem is the physical size of the project. Furthermore, remember that Mac OS includes hardware drivers, interface management, drawing routines, scripting, printing, networking and so on. I don't believe there are many developers who are equally good at every aspect of a modern OS structure, because the knowledge required for making a single system component is great. The sum range of knowledge required for building a working OS is inconceivable, while an OS 9 team is very small.
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Make no assumptions