Let's clarify the Save game situation. If you are wanting to trim, or pare-down the number of Saves in your game, you use the Save Game dialog, or interface, to do that. If you instead use Windows Explorer, the game gets confused by that.
If instead, you want to "clear" the Save data to begin anew with the game, you delete the Save folder with Windows Explorer, generally the C:\Users \UserName \Documents \SH4 folder. Going from the way you describe, it sounds like you used the Save Game dialog to attempt to clear the Save folder, which leaves the main part of the game still in there. Nothing gets updated or cleared like that...
The idea behind copying the Save folder data and putting it elsewhere is so that if clearing the game's Save data by deleting the folder with Windows Explorer didn't work, you then had a back-up with which to restore what you had, if the deletion didn't work... I hope I didn't talk in a circle again... I confuse myself with verbosity...
