It sounds like you are creating a new document (drawing) as the final output of your efforts. One of the first questions to ask is: have you completed the modeling of the second configuration? If you have not, I have found that using the "Duplicate Objects..." function in Pro/Intralink gives me the biggest bang for the buck. When you execute this on the .drw file of the original, this will give you the option to create a new Pro/E object for just the drawing, drawing & assembly, or any combination of newly renamed components within. Be careful that you don't copy your library parts (such as fasteners, etc.) unless you truly intend to make a new library entry, or unless it is your company's policy to have all items associated with a particular assembly dedicated to that program.
If your new configuration is a member of an assembly family table, I would suggest a slightly different approach. With the original drawing active in Pro/E, do a "File/Backup..." to an empty directory on your local hard drive. Exit the drawing and erase the original from session (File/Erase/Not Displayed...). Change working directory to the new folder that contains the backup. Open the drawing, RMB and select "Properties", then use the Drawing Models/Add tool to select add the alternate instance the drawing, then then use Drawing Models/Replace select to be active. Once you have updated the views you may delete the previous instance from the model list, save and make any alterations required.
The resultant objects will be an exact duplicate of the original, with the newly renamed assembly used in all previously defined views. There is no assosiativity to the original drawing file, so you can alter the copy without impacting the object it came from.
Ed Leitkowski
Staff Engineer
Rock Engineering, LLC
South Windsor, CT USA