Maybe something for Nathan?

Did you install such that C:\tmp\blender\blender.exe or C:\tmp\blender.exe?

If you installed with C:\tmp as the installdir, then yes, the installdir gets completely removed - Installing into a dir without a creating a subdir, so installing directly into a directory that's already used sounds like an odd thing to do anyway. I'll make sure that the installer gets clear notice that the _installation directory_ gets recursively deleted. And on install that one should ensure there is _at least one_ subdir for Blender alone, not containing previous files.

Until it was mentioned in the forums, I had not paid close attention to how the custom install worked.
I had usually just installed it the standard manner, which creates its own Blender directory under Program Files.
I guess I assumed that it would create its own Blender directory in whatever location you chose... now I am surprised that it doesnt.
I guess I also assumed that an 'uninstaller' would remove a list of installed files, not just *.* on the install directory.

Fixed the installer to only delete files that were installed, leaving the others intact.