What are you trying to do exactly? Are you trying to export or import save data? Not all games have their saves as "Save Data", plenty just save as "Extra Data" (eg: MHGen/XX/Stories/USUM/etc.). You can't import or export extra data from a game that doesn't support them. But I don't know why Checkpoint would freeze since it automatically decides what data the game uses... Just make sure there IS save data before you do anything, if there isn't (eg: haven't played the game at all yet) it obviously won't work.
I'm trying to import the save file from Pokemon Sun. I wasn't referring to any file just what JKSM has named the primary file import function. Oddly the secondary import function works, and luckily Fire Emblem Fates has save slots that write to the ExtData. I can't even boot Checkpoint, as the freeze occurs when I try to launch it from the homebrew launch screen