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