In reply to arctickev:
Go to TOOLS - OPTIONS - ADVANCED - CONFIG EDITOR
Go down the list until you find "mail.root.pop3"
This appears to be the config value that tells Thunderbird where to find the mailboxes. I cannot find another value that defines the name of only the '.default' folder so this seems to be defined here too.
The 'value' should be an address on your C drive.
Double click on the value and it will return a dialogue box in which you can view the entire address. It should be an address like the one I posted earlier, probably ending in '.defaultMail' (no backstroke at the end).
Check that there is a substantial set of configuration items for each of your mailboxes. They will have id1/id2/.. etc in the 'Preference Name' and you will recognise some of the values as being related to you email addresses. If Thunderbird is correctly pointed to the mail folder and has configuration for each mailbox one would think it would work. I am not certain though. You might still have to create accounts. If you do, then you can point Thunderbird at the existing mail folders in ACCOUNT SETTINGS - SERVER SETTINGS - LOCAL DIRECTORY.