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Found a weird bug. When I log in and hide a Nintendo game from my profile the changes reflect while I'm logged in. Once I log out and view profile they re-appear.
In order for changes to apply while logged out, the linked account needs to be verified. So this is technically not a bug, it's a safeguard from others making changes to accounts they don't own. Unfortunately, there is not an automated way to verify Nintendo accounts yet.
I am not sure how to implement it yet - on PSN for example we have the user enter a code in their About Me, but Nintendo doesn't have anything like that...
Anyway I manually marked your account as verified, so it should keep the games hidden while logged out now.