I used savemii to backup my saves as well as system config tool. I then use saviine to restore them. I know that app very well, but you must have a save on there afaik, and it can only do one save at a time. the system config tool version I have has a backup utility but no restore one (not sure why). savemii is supposed to be the easiest way. however, I don't know much about actually restoring everything. both savemii (possibly savemii mod, whatever the difference is) and system config tool can batch dump.
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btw, saves don't appear to be encrypted, so restoring them with any of those programs works (interchangeable). however, some use the serial id to differentiate the files, like system config tool, or the title id, like saviine. you may have to look them up if you're restoring one save or something.
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alright, I just checked. savemii mod uses content id (just like saviine and just how it would appear on the system). only system config tool uses the product code (not serial id, which is product code+company code's last two digits).
