For the future: This happens when it can't find the wiiu/apps/NUSspli
folder on your SD card, so make sure you have that folder and that the NUSspli.rpx file is inside of this.
So yea, moving the rpx file out of the folder and removing said folder breaks auto-updates. Not much we can do as there is no way to get the path of the currently running .rpx file, so we have to hardcode it.
With Aroma and NUSspli.wuhb it's different though: Aroma allows to get the path of the currently running .wuhb file, so we can exchange it no matter what.