What follows is base upon my own experiences of (successfully) fixing OE problems (by trial and error), rather than any 'text book' methods. Use at your own risk!
All OE folders have the 'dbx'file extension. Run a search for *.dbx. If you're in luck you will find (for example) that you got two files called 'inbox.dbx' on your PC. Look at the dates (and the file sizes) to see which is the 'old' file and which is the 'new' one. Right-click on the old file and select 'copy'. Then right-click on the new one and select 'open containing folder'. Right-click within that folder and select 'paste'. When you're warned that a file with the same name already exists, accept the option of over-writing it. (NB: That will delete the content of your 'new' inbox'. If it's already got mail in it, copy those mails to another folder before following these instructions!).
Repeat for other folders. If you had a folder called, for example, 'business' on your old installation of OE which doesn't appear in your new installation, create a new (empty) folder with that name before following these instructions.
Chris