Close down Opera and edit operaprefs.ini in the preferences folder (see help -> about Opera for the location). Under the "Mail" section in the file, Remove the "Mail Root Directory" line so that Opera uses the default mail folder location. Or, if you have your mail folder is a non-default location, make sure the mail root directory path is correct. As in, it points to the mail folder you were using before (not the new one that Opera created in the default spot).
Also, did you manually upgrade by downloading the installer and running it? If so, did you click "options" and set the "install path" to your existing Opera folder so that the button said "upgrade"? If not, you might have installed Opera to a different place.
What OS and what version did you upgrade from?