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That's a successful version of the Pyramid story. NT had been developed alongside OT (or whatever the old tech kernel was called).

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.

NT was created in parallel, and run in parallel for a long time. Eventually the benefits of NT outweighed the 9x kernel, and computers were fast enough that the extra overhead was acceptable. 9x was EOLed and XP went with the NT kernel.

They were two different products that ended up converging enough that sharing code made sense.

If there is any lesson from OS X and Windows, I think you've hit on it, exactly. The way to replace isn't to stop one and start another – instead, you need to build in parallel and have a smart migration plan.

Yes, but they had been developing the NT product line for years, so it wasn't a full start over. Then they had the Windows 2000 release which was their first stab at a "merged" kernel for desktop and pro/server. XP was the full cutover after Windows 2000 validated that it'd work.