Transfer “save data” from Wii-mode to “Wii U-mode”

Commonly with virtual console games, you can hit the center button (Wii menu?), and exit the game. This will automatically save the state of the game. Next time the game loads you'll begin at that spot; however, after reloading once the save state is no longer available -- resetting the system won't allow you to resume from that state again.

No, you won't. The disc slot acts as a "variable" piece of software. If you check your save data in the Settings, everything to do with a specific piece of software (such as the Wind Waker HD, which I have both digital and physical copy), will be placed in the Wind Waker HD "folder," including the save-data for each user Mii and the software itself. If you want to have 2+ separate files, just create another user Mii on your Wii U. However some games, such as Game & Wario, are "universal" and all the save-data is shared throughout the Wii U. In order to get an entirely different save file for that, you basically have to get another Wii U (but Game & Wario has 12 in-game save files shared by everyone, just as the Wind Waker has 3 in-game save files shared by only that user) .