Signing a file generates a long hex number that is used to verify that a given file has not changed. Any time a single bit in a file changes, the signature completely changes. This allows an OS to check for tampering. (in this case, the 3ds knowing you've been screwing with it's saves)
This signing process (and encryption) must be done on a 3ds because the algorithim to sign files lies hidden somewhere on the 3ds SOC most likely.
You can get around this be using the savedatafiler dev tool to decrypt and modify saves (it's warez - can't link here). Google for it and how to use it.