I never used smooth save, but i suppose it works the same as playerprefs in that regard. Let's say you have a coin as a pickup. You set a prefs key for it, for example "Coin1PickedUp". It would be a bool, with a default value false. When you pick it up, you will write the value true to that prefs. Mext time you load a scene, before it's created, the coin will get the prefs and bool test it, if it's true, it will get destroyed (or not spawned if you use a spawner for it) if it's false, it will be created or it's renderer enabled or howevwr you want to organize it, but for performance i propose creating spawners instead of coins that will spawn the coins or not depending on the prefs.
If your game starts anew when you quit, reset thise prefs to default before quitting.