Theoretically, you might be able to do this using liomajor's .3ds/.3dz to eshop save tutorial...
You would need to use the tool linked above to make a copy of your rom as a card 2 type first, then put it on your gateway.
Then try this, maybe it will work:
1. Backup card 1 rom save as an eshop/decrypted format by following liomajor's .3ds/.3dz to eshop save tutorial
2. backup the save on your pc somewhere
3. Play the card 2 version of the rom then make a save.
4. Then while the card 2 rom is mounted, backup the save using savedatafiler by selecting CTR CARD
5. Replace everything in the card 2 save folder with everything in the card 1 save folder that you made in step 1.
6. Mount the card 2 rom again
7. Go back to savedatafiler and go to the SD tab and import your save again
8. Play the game and see if it works