After loading the level - it will be as you made it in the editor. Everything you did during the game - is not initially taken into account.
Your save system should keep track of what world items are in your inventory and remove them from the level after loading if they are collected to prevent them from being cloned.
No, all that is there initially in blueprint is a “Save Game” flag for variables (which initially has no effect on anything).
With it you mark which variables need to be serialized, then you add this data to the save file.
This is described here in maximum detail.