The .sav you created with a card1 game won't be touched by that conversion. You didn't lose your savegame but you havn't it in the card2 game either. It's laying on the SD Card and won't be used.
If you want to get it in the card2 converted game, follow this tutorial to extract the save files from the.sav, used in card1 game:
http://gbatemp.net/threads/tutorial-export-import-save-games-to-3ds-3dz-retail-carts.391154/
The step you have to follow is Step A. Then you have extracted the .sav file.
After that you load the ROM from your card2 game and just import the extracted save into the CTR Card.
Thats it. So you can ex/import your savefile
If you need help, I had to use it since I want my saves in card2 games, too.
P.S: I thought it would be nice that a conversion from card2 to card1 didn't erase your save.
Look, if you don't delete it, the game doesn't work after the conversion. That's the reason why it has to be erased. But I can try to write a little bit extra code for that script to copy the data that will be erased into a separate file or something like that.
I don't know if this is a valuable savefile. That needs some research. But if you want that feature I will try my best to realize it.