If you had a backup of the "mail" folder, you'd look in the store/accountN folder for the account. There each message is stored in a mbs file where the mbs files are sorted by year/month/day/number.mbs.
You'd then search in day folder for the mbs file that contains the message you want. You'd then open the file in a text editor to see if the attachment data is still there. If it is, you could then import that mbs file into opera via "Menu -> settings -> import and export -> import mail -> import generic mbox" where you choose the mbs file and choose what pop account to import into.
If you don't have that, you're going to have to open the "File" file in a text editor to see what it is. To be useful to you, it'll need to be in mbs format and contain the message you're looking for where it has the attachment data with it. If that's the case, you can then import it like you would an mbs file from the store folder. If the "File" file, is something else, you're out of luck (unless it's an eml, file in which you can convert it to an mbs file).
See this page for how to fix it. (Save the mhtml file and and open it locally).
Or, do you mean you used Thunderbird to fetch all your mail.opera.com messages and you need to know how to restore them in Thunderbird because Thunderbird is messed up?