Problem is it's hard to pin down what causes the ban, in your case you would have to run CFW, Checkpoint and you would have a modified save. Does the game go online, are you restoring a clean nand after using checkpoint.It's why I'm asking if there's been any cases of bans.
If that save goes online in some form I would be prepared to take the ban should it come, say it's a pokemon or smash save or something.
If the game is a strictly single player game and you're restoring a clean nand I would think it's fine but there's no guarantee, chances of being safe decrease if you don't restore a clean nand.
I have been connected to internet with cfw, opened homebrew channel and been connected to internet on an emunand that didn't match my sysnand full of Nsp's. That was over 3 months with no ban. However, I never played or updated an nsp connected, had error reports off and never modified any saves or anything on my sysnand. We just don't know what you can and can't do.
You take a chance of being banned doing anything, you either accept the possibility or you don't do it.