I'm unclear what program you are using that you are trying to SAVE.
Keyrite and Vogone create NEW files so they don't overwrite your original. Thus, they always are doing a "Save As" operation, not Save.
This allows you to make a change, save it and compare it to other files with different changes to the same original. Then, you can see which is the best.
If this didn't help you, please ask again and be very specific about what program you are using, and what it is you want to do. Once we understand the question, we can provide an answer.