There is no need to convert.
Every half decent DS flashcart uses raw .sav files that work on everything that uses raw save files (retail carts included.)
(Besides, DSTwo isn't in the output list in that converter.)
^ What they said above.
All flashcarts have a default save file of .sav and it's fully transferrable to another flashcart. I had a knock-off R4 clone and transferred my .sav files to my Acekard 2i and everything worked fine.
well if i bothered to check before i posted the converter link, i would have seen that all the supercard flashcarts are in the same category as the acekard
I've had so far an R4, Acekard 2, iTouchDS, and ultimately Supercard DSONE, plus exchanged files with a friend who has an M3. All of them supported save files from one another with absolutely no issues or conversion required. My guess is MAYBE on the various firmwares a few savegames will be handled at different sizes and potentially not read, but as long as your savefiles are 512KB you should be alright.
You hate to lose saved data? Backup before experimenting.
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