Creating an instance of a ScriptableObject, that will not change the base asset.

If you don't want to keep each INSTANCE of "Sword" stored as a scriptable object, you will need to save those values yourself, somehow.

I would suggest this be done by storing whatever "contains" the sword instances (e.g. player, map, npc, whatever), as a scriptable object, that has a (serializable) list of "Sword" objects, each with its own individual values.

With this method, you would create an instance of your SwordA (think of it as a prefab), then add this new instance to your player/map container object, and apply all your "bonuses". Then simply save the player/map itself as an asset, rather than saving the sword instance itself.