From MozillaZine Knowledge Base

If you have accidentally deleted one of your mail accounts by clicking on the "Remove Account" button in Thunderbird, this does not mean that your mail has actually been deleted from your computer. That mail should still exist in a child folder in the Mail folder in your profile folder. (This assumes that the account is not using the Global Inbox, in which case its mail would be stored in Local Folders.)

Once you've gone to your profile folder and verified that the mail for the deleted account still exists, do the following to get it back into Thunderbird. You may wish to make a temporary backup of your profile folder before proceeding.

1. Start Thunderbird and create a new mail account, using the same email address and server settings as the account you deleted.
2. It will create a new account directory with a numeric suffix. For example, if your old mail account directory was pop.gmail.com it will create a pop-gmail-1.com. Use the browse button in Tools -> Account Settings -> Server Settings -> Local directory to specify the old account directory and restart Thunderbird.
3. Check the accounts inbox folder to see if it has messages. If not then you probably specified the wrong location and need to use the browse button again.
4. Its recommended you leave the account directory that you created in step one alone - it only wastes about 10KB due to several default files that Thunderbird created. However, you can delete it (after exiting Thunderbird) if it might cause confusion later on.

If for some reason this doesn't work you can import each folder using the ImportExportTools extension. Each folder is stored as a text file with the folders name and no file extension (a mbox file) in a directory named after the accounts mail server in the profile . For example, if you wanted to import the inbox folder for gmail you'd select the "Mail\pop.gmail.com\inbox." file. Ignore the inbox.msf and inbox.sbd files.