I only changed the secure value of the user2 file, and it successfully loaded up the profile after re-encryption and injecting.Did you only restore the user2 with updated secure value? I don't think a single game has the rights to have more than 1 secure value for its files, probably the user1 and user3 files already had the latest secure value or you did only restore the user2 file.
I see what you mean about a game not having more than 1 secure value, but even so, the other profile that my brother has (he has two in his game) showed, in the profile selection screen, as a working save file (it shows name, stats, play time, etc.). Then again, he hasn't opened the untouched profile; so I'll ask him to test it.