I don't have a CMOD setup right now.
But I think you can add the new field to the existing folder as well and do the mapping with the application group field in the "Field Mapping" tab of Folder. That should suffice. There's no need to create a separate folder unless you want the end user to access the old and the new documents through different folders.
Also the field value for this newly added field for all the old documents would be NULL.
In case if that doesn't work and you still want to maintain the old folder for accessing the old and the new documents; what you can do is copy the existing/old folder, add the new filed to this new folder, save it.
Then rename the old folder to something else, eg. Folder_Old.
After that rename the new folder to the old name, eg. Folder.
Confusing indeed
Hope that works for you.
Cheers
Pankaj.