Nope. Mine are stored on the normal partition.
that is strange.... file change dates indicate, that I didnt save any games for at least a week, so I assumed, that the new saves ere all stored in the emunand partition o.O ..... so basically I could just do full backup for safety, the backupjust my save games, format the whole card to get rid of the corrupted files and then only copy back my saves? sounds too easy to be true, lol ... gonna try that now
edit: unbelievable, its still not working...
well, first of all, you were right, all save files are stored on the normal visible partition
here is, what I did... just to be safe, I made a full backup of the whole card using win32diskimager
then, seperately I backed up my gateway savegames
then I formated the whole card (whole, not just visible partition, but whole card, including emunand partition) to have a clean new setup and let the 3ds set up the new card (language, country and that whole stuff), then I backep up those settings ("Nintendo" folder), ran the gateway installer and then ran the gateway exploit and had it format the card and set up emunand partition
then I put my savegames and the backed up "Nintendo" folder with the system settings back on the card, then I used the emunand backup/injection tool to inject my old 6.3 emunand (I made that backup earlier today to test this new tool)
problem is, games still crash, when I enter new locations... so file corruption is probably not the case, because all files are new except the save files and my 6.3 emunand
so could it be a gateway problem? :/ is my card failing after all?
edit2:
tried a new sd card. just copied the save files and the launcher.dat on it to safe time and totally ignored setting up emunand, because it is not really needed to just test out the card itself
so I ran the games with 4.5 sysnand and they still crash, when entering new locations X.x
so basically, it has to be a gateway issue now, right?
