Replace and new are different.
Whatever method you choose to get the new - but same name - file / icon on the box - Fences should still have it where it was (in a Fence or not) because it has the same name.
Is different... What you want is for a rule that you create in Fences to be scriptable and, as far as I know, that is not possible. I will get with the lead dev to verify, however.
Basically it would be that you place a file on the desktop and script running a Fences rule to get it into a Fence.
Ill let you know if it can be done after I hear back from the lead Dev
Stardock Support Manager