Not quite the same thing, but both Windows and MacOS at one time had a somewhat annoying warning at startup, asking to format a partition if the file system was unrecognised by the OS; so, basically, any file system that was not native to the OS concerned.
Of course the real danger with that was that Johnny DF would boot their machine, see the message, and think “Hm, OK, I’ll click that…Yes”.
The only way to avoid the message was to remove the disk, format the partition with a known file system, or prevent it from mounting - the latter was my personal workaround, gleaned from years of mult-booting experience.
As far as I’m aware, the issue hasn’t existed on Windows since XP, or possibly 7; and early-mid versions of MacOS (X).
If an “in-place upgrade” is performed (from within Windows) it should upgrade the existing system, with the pre-existing layout. If the Windows Installer DVD/USB is booted, then Windows is replaced in its entirety.
In that case the user should carefully plan their strategy, as Windows has never supported the concept of multi-booting with Windows and some other OS on the very same disk.
With inexperienced hands there is always scope for things to go awry. For this reason, I always recommend (wherever possible) to install each OS on a separate disk;