It doesn't matter which files it contains - it should still work by transferring.
First, make sure that both the memory cards are in. Then switch your Gamecube on without a game disc. On the screen that comes up, move to the "Memory Management" (don't know if that is exact wording) menu, and press A. That will take you to a screen which shows both memory cards, and the files that are in both of them. If you want to transfer one to the other, press A on whatever file you want, then press A on "Copy". This will transfer it to the other memory card. You can do this with all the files, then keep the other memory card so that you still have your files if the other one gets corrupted.