Are you using sysNAND or emuNAND?
When you normally play with a stock Switch the saves are in the system memory. If you set up an emuNAND and and you use CFW only on it you will see all save files with Checkpoint (part of the copy of your sysNAND), but every changes you make WILL NOT REFLECT in sysNAND, they are completely separate.
So, if you want to make changes on your "traditional" save file, you have to run Atmosphere in sysNAND (do this at your at your own risk, I personally suggest to use Atmosphere only when you have to use an homebrew software and in airplane-mode).
If you want to use only emuNAND, you have to play your game entirely on emuNAND (without online connection).