I'm sure there are a lot of file management programs around, but what I have done is copy each drawing to a separate directory named "Transmitted" when it is plotted for submittal. I change the attribute to read only using Windows Exploring; right click on the file, choose Properties, and check Read-only Attribute. Before copying, I change my PE seal to a block that says:
THIS DOCUMENT ORIGINALLY ISSUED AND SEALED BY name, REGISTRATION NO. number ON date. THIS MEDIA SHOULD NOT BE CONSIDERED A CERTIFIED DOCUMENT
At the end of the project, I copy everything to a CD-R.