The fail is usually random, I don't think it's related to the NNID, but maybe it is.
Continue to do it with the non linked account, see if it fails or still work fine after few days.
About your question :
1) I'll go the long answer:
The console is using two different folders to save a savegame : one private (linked to the Mii ID) and one common (for shared data, like unlocked tracks that other family member can enjoy, etc.).
Loadiine has two different modes for the savegames :
- Acting the same way that the console (one private per Mii + one common folder)
- Not caring about accounts at all, and using the same savegame whatever the selected MiiID is.
By default, loadiine is set to the "shared" mode. all users are sharing the same game progress.
so, if you never changed the settings and if you started playing a game with your Mii linked to NNID, then you can continue playing it with the Mii not linked to NNID.
in case you set the save mode to "unique", you can convert them to "shared".
1. set the save mode to "shared" in loadiine settings
2. on your SD card, rename all the wiiu/saves/game title [ID]/
common -> c
800000xx -> u
(rename the "common" to "c", and the folder with the number to "u")
2) About the updates
You can replace the original files with the update files. it works fine.
But in case a new update is released and break compatibility, you might want to revert to the "clean" game state or previous update version. replacing the files is not the best method to revert files.
Loadiine let you put the updates in a sub-folder, and load the update files in realtime.
Advantage of replacing the files : you are saving space by replacing files.
Advantage or using sub-folders : you can switch different update version, and revert to a previous version. (MK8 for example doesn't work on MiiMaker if you have an update, but works fine with SSB Mode)
disadvantage of replacing the files : you can't revert the version to a previous state if you didn't keep a clean game copy.
disadvantage of using sub-folders : it takes space on your SD card.
If you are using a game mod, for example a fan translation, or game hack to get new tracks on Mario kart 8, then it's better to use the sub-folder method. This way, when a new patch or mod or hack is released, you only replace the sub-folder, you don't have to repatch the game.
I don't know why Tokyo Mirage uncensored patch is not using Loadiine's update method instead of forcing the users to keep and repatch the clean game every time as they are providing the game files in the patch release.