Can you transfer fossils from Fossil Fighters into super fossil fighters

Yes, but it only works in that direction. In order to do this, you'll need two DS systems, a copy of Champions, and a copy of Fossil Fighters.
1. Boot up the original and travel to the Park area with the Fossil Rock(s) you want to transfer.

2. Talk to the excitable Attendant by the completed Fossil Cannon to load your Fossil Rock(s)

3. Save and quit.

4. Clicking on the file you loaded the rocks on, go to "Play with Another Person."

5. Click Battle/Trading. Click "yes" at the notification.

6. Boot up Champions. Go to "Multiplayer."

7. Select "Local Play." "Yes" at the prompt.

8. On Champions, click "Receive Cannon Fire."

9. Select "Fossil Fighters Cannon"

10. Go back to your copy of Fossil Fighters. Select the name of your Champions character. Click the Fossil Rock(s) you want to send, and then hit fire.

Ta-da! The Fossil Rocks are now on the Fossil Lawn on Ribular Island!