I just tried Captain Toad with the latest server version again. It still kills my save. I finished the whole game with the non server version and had no issues. Now I ran the server version again, it will load up the save but when you exit the game and start it up again you will start from the beginning, i guess it's somehow coruppting the save.
I attached a log again, the filename of the save is GameData.bin. Not sure if there is anything to see though.
The only thing I am thinking is your save is auto created or loaded and the accounts userID is linked to the save. The different loadiine versions must appear as different userID's to the WiiU. If it don't match the ID of the save file the game makes a new one for your ID and in the process overwrites the old one, as loadiine only writes to local u and c folders, ignoring any userID.
Saviine killed my captain toad save which was a modified cafiine boot with original disc. Save just wasn't there on game boot and never returned. The wiiU did this when I first got the game without explanation as well. Only thing I can think is one save per system, but nintendo don't care about different profiles on the system. I'll un-install 1.1 update and see if profile A save will be overwritten by profile B.














