Do you have any examples of Microsoft throwing away their codebase and starting fresh? I believe that is what Apple did with the OS9 to OSX transition. I can't think of too many examples where starting from scratch worked out though.
It's hard to say whether Copland was a rewrite or a refactoring, but what is indisputable is that the root architectural decisions of Mac OS were a dead-end.
They actually had to go beyond a rewrite to build something completely new and different, and then retrofit an emulator onto it to support the old system.
"Microsoft almost made the same mistake, trying to rewrite Word for Windows from scratch in a doomed project called Pyramid which was shut down, thrown away, and swept under the rug. Lucky for Microsoft, they had never stopped working on the old code base, so they had something to ship, making it merely a financial disaster, not a strategic one."
Even that wasn't "starting fresh". The starting point was a complete operating system: OPENSTEP. It was just a different operating system than the one they were using before.
They wrote a new system in tandem with maintaining the old one and when it was mature enough, swapped out old for new. This pattern is very commonplace.
They were two different products that ended up converging enough that sharing code made sense.