reinstalled and it just acted as if it were to be re-created, so the save is directly connected to the cia which is kind of disappointing but I didn't do too much on the save relative to visible progress.
basically this is the scenario: you install a cia that you installed before that had a save, but you didn't mean to start the install, so you cancel it, which deletes the cia (or installing the cia while you already installed it deletes it more than likely) which in turn deletes the save.
all I lost was some grinding on star sapphire, I just ripped my cart and decided to turn it into a cia so I could just install the modded version. Shame.
Thanks for the responses anyway, too bad on the save, I'm just gonna pkhex some of the grinding back I suppose lol.