I am confused as to what you are trying to achieve.
Do you want to just backup your folders? In this case just copy them to a backup medium, not the same hard disk.
Do you want to backup your dbx folders and then remove them from OE but still have access to them?
Possible but tricky.
You will have noticed that OE produces a dbx file for each folder regardless of the folder's original location in the tree structure. If you have folders with duplicate names then OE appends a number to the end.
For clarity's sake, rename your folders to something like June99. Now close OE and back up.
open OE and remove those folders you want to clear out.
If you decide you need access to an old folder, you need to recreate a folder with exactly that name in OE. It doesn't matter where you place it. Next copy any old email into it so that OE creates the dbx file.
Close OE and overwrite the newly created file with your old one.
I am not sure, but I think I have had problems with attachments in the past, but that was after I had formatted my hard drive. So back up your attachments first.