If you have a Pop mail account, then it will look at Inbox on server and download anything not previously downloaded and mark everything as new unread mail. This is because TB Pop mail account has no knowledge of any marking/labelling etc that has occured on the server. It merely downloads to TB because it is a Pop mail account. If you have an IMAP mail account, then TB is remotely viewing folders and emails on the server. You see folders because you have subscribed to see them. When you select to view an email in a subscribed folder, the contents are downloaded to a temporary cache to faciltate quicker access to emails in that folder, but the cache is deleted when you exit. So these emails are not stored on your computer. You can also synchronize folders to keep a local copy on your computer, but those folders will be updated/synchronized when you make changes, so that both TB folders and server folders are the same. Whilst a copy is stored on your computer any changes you make via webmail or TB will be reflected in both. So, whilst synchronizing gets a local copy on your computer it cannot be relied upon as a backup as the folder is constantly updating with server. So it depends upon what type of mail account you are using. If you have an IMAP mail account, you should be seeing the changes you made on the server.