Had this same thing happen to me, and yes,it is very confusing. I bought a new Wii U to replace my other one that was dying, thought I was going through the correct process and the next thing I knew all my content was gone from the Wii U AND my 3DS. The way it was worded when I was going through the deletion process made me think that it would only delete the ID from that system. I know it was partially my fault, but it's so stupid of them to have an option like that...why would anyone want to delete their content beyond saving like that?
Anyways, after like an hour on the phone with Nintendo and escalating to higher management I was able to get them to retrieve most of my stuff,including ambassador games. I really had to persuade them to do it, like mention the fact that if they didn't fix it I would never purchase another Nintendo system or game again. They blamed me for not reading the instructions properly but when I asked why they had such a backwards system in place in the first place they couldn't give me a single answer. It takes about a week for your stuff to reappear, and instead of DLC and Virtual Console games they just gave me eShop credit.
Anyways, after like an hour on the phone with Nintendo and escalating to higher management I was able to get them to retrieve most of my stuff,including ambassador games. I really had to persuade them to do it, like mention the fact that if they didn't fix it I would never purchase another Nintendo system or game again. They blamed me for not reading the instructions properly but when I asked why they had such a backwards system in place in the first place they couldn't give me a single answer. It takes about a week for your stuff to reappear, and instead of DLC and Virtual Console games they just gave me eShop credit.