I'm going to assume you went into the Supercard firmware to back it up. Check your microSD to see if the save file is there. There's a possibility your Supercard could have a faulty battery. I believe it saves to a hardware feature called PSRAM, which is known to become corrupted in a Supercard DS-One (and the manufacturers refuse to fix).
To check your psram, Hold L+R+Up as your DS boots, keeping it held down as it boots past the health warning. It should enter a white screen with some text. Press A past some dialogs, and then get to a screen where it's counting some data values. If yours says something similar to this, you've got a defective Supercard-
PSRAM error! cell error
addr=00000000
The address can be any number, but if you have the error at all, it's got a broken internal battery. Ironically, this issue has become a non-problem if you happen to be able to patch the save. But you can't do that sadly with this game.
The other issue is that the battery may just be dead and cannot hold data anymore. This happens with some slot 2 GBA cards, they'll die after a year or so of use. It might seem to save, but once you switch the power off, it might lose the data. The only solution is to either get a new flashcard or try to change the internal battery. The latter option is likely too much trouble, and not worth the hassle.
To check your psram, Hold L+R+Up as your DS boots, keeping it held down as it boots past the health warning. It should enter a white screen with some text. Press A past some dialogs, and then get to a screen where it's counting some data values. If yours says something similar to this, you've got a defective Supercard-
PSRAM error! cell error
addr=00000000
The address can be any number, but if you have the error at all, it's got a broken internal battery. Ironically, this issue has become a non-problem if you happen to be able to patch the save. But you can't do that sadly with this game.
The other issue is that the battery may just be dead and cannot hold data anymore. This happens with some slot 2 GBA cards, they'll die after a year or so of use. It might seem to save, but once you switch the power off, it might lose the data. The only solution is to either get a new flashcard or try to change the internal battery. The latter option is likely too much trouble, and not worth the hassle.