Question / issue 1:
I was attempting to backup my Sky3DS+ save and use it for the same game after installing as a cia. I could not find an easy way to do it, since after I installed the cia Checkpoint failed to display the game at all. (I'm using Mario Kart 7 as my example.) Checkpoint also seemed to be corrupted and periodically crashed.
I think the problem was Checkpoint is confused when you backup from a cart and then have a cia-installed game that is the same ID. It seemed to be corrupted and not show the cia-installed version at all. I deleted all the cached data in the SD:\3ds\Checkpoint folder (while copying out my original save first). Then I ran Checkpoint and it pulled in the cia-installed games properly. Finally I shut down, took out the SD card and manually copied the original save to the backup folder made from the cia version. I booted back up, started Checkpoint, and restored that file. It worked.
It seems like a pretty convoluted way of doing it, so if anyone has a better idea let me know.
Question / issue 2:
If I use the save from Sky3DS+ (which was originally generated using my own cartridge dump and private header) will the header also be safe to use online when restoring from Checkpoint? The cia I installed was created from the .3DS file that I dumped from my cartridge. I don't want to put myself in position to be banned when playing online.
Thanks!