Just want to add something here.
1. Purchased Shovel Knight a long time ago. Installed on NAND.
2. Installed some games last week with Brazilian. Of accident I installed Shovel Knight as I forgot I had it for Wii U. This was to the USB so I had 2 copies of SK installed.
3. Removed the USB-version (Brazilian).
4. Found this thread and wanted to find out if it effected my mishap so I deleted the NAND-version (Legal).
5. Re-downloaded and waiting for the fail but it installed successfully.
Seems strange? Was it because one was on the USB and the legal one on the NAND?