Ok, if you want to combine all your accounts folders into one set of folders, you will need to choose the Global Inbox option. First back up your email messages then move the messages that are in the accounts that you want to change the folders of to the Local Folders, then click on Tools > Account Settings, then under that email account click on Server Settings, then click the Advanced button and select 'Global Inbox'. Repeat for every account you want to change the folders of.

Hope this helps.

In that case I would suggest that you totally remove the third account from Thunderbird, reboot, then create it again from scratch. But before you do that 1) move or copy any important email messages from that account to a folder in another account or just save the messages outside Thunderbird, and 2) write down the account settings so that you can use these settings when you create the new account.