Yes, it's safe as long as they're the same release (which they are in this case) and you installed to the same partition (
When you boot your computer it will still offer a choice between Windows and Xubuntu but it will boot whatever is on the
root.disk. If you wanted to change the boot entry back to Ubuntu you'd have to use
easyBCD (for Windows 8/7/Vista) or edit the boot.ini (Windows XP).
Wubi boots via
wubildr.mbr) and a version of
wubildr. What they do is locate the first
/ubuntu/disks/root.disk it finds on any partition, and then load the Grub menu (
grub.cfg) from within that
root.disk. So it doesn't matter what is on that
root.disk (or even what partition, provided in the
grub.cfg it has the correct partition
UUID). So if you installed on
C: it has to be on
C: or you have to manually edit the Grub menu entry before booting.
The only issue is that the modules built into
wubildr must be compatible with the
grub.cfg so changing releases can lead to incompatibilities. In these cases you can sometimes manually boot from a grub prompt, but it's best to stick to the same one to avoid issues.