i think there are ROM dumpers that can also do hotswapped save insertion? but the slot2 version was the one i use before (inserted a save file into retail Strange Journey, because my playthrough on that is insanely long).
I think it's the NDS Backup Tool. not sure which of the three (there's 3in1, Slot2, and Wifi versions), but i think all of them can copy/insert saves from/to retail carts. the first two need to be run from slot 2 though, and the third requires an FTP server running off of a computer with wifi connection.