http://en-americas-support.nintendo.com/app/answers/detail/a_id/1125/p/431/c/266
The following is not transferred during the system transfer process between a Wii and Wii U:
- Software that is present on both consoles
- While the software will not overwrite what is already on the target Wii U system, the new save data will overwrite what is on the Wii U
It's looks like that while your 100% completed Xenoblade on your Wii console will be safe, but your Wii U save file will be deleted during the System Transfer.