That wouldn't necessarily be a problem, though. They wouldn't kill the Win32/Win64 APIs or anything else that people tend to write Windows applications to, they would just replace NT with Linux and adapt the Windows APIs to run on Linux (basically WINE, but presumably Microsoft could do a more complete/compatible job due to all the institutional knowledge they have).

Some apps still wouldn't work, like anything that calls NT APIs, but they could make that work with a compatibility layer until they're ported.

I agree that this seems a bit unlikely, though. But who knows where their priorities may lie in the future?

A significant amount of businesses worldwide are still run on Excel sheets and Access databases on SMB fileshares. Combine that with an insane amount of VBA code and you have something it is very hard to justify why you should spend time and money porting or virtualising when you can just keep it running on Windows. I work with very large banks and insurers and see this everywhere. Justify effort / cost / risk / benefits of that vs investing in new customer / ‘digital’ stuff that will actually sell more.