Imap mail accounts keep the emails on the server and you see a remote view of those emails and folders. When you subscribe to see a folder, the headers are downloaded, when you select an email to read, the entire folder is downloaded to a temp cache facilitating quicker access. If you synchronize folders, then a copy of that folder is downloaded to an mbox file in your profile, so that you have a copy of the server folder. When you make any changes to a synchronized folder, read an email, delete or move etc, then Thunderbird will resynchronize with the server to update the server. A synchronized folder allows you to work in 'offline' mode and this is the best time to perform a backup as you know there is a temporary stop on synchronizing as you are offline. They will resynchronize when you go back into 'online' mode. So, with IMAP mail accounts, the folders you see in Thunderbird are the same folders on the webmail server. If you make any changes via Thunderbird or webmail then you are changing the same folder. You cannot delete an email without deleting it from the server, they are one and the same. What you can do is move/copy an email into Local Folders and delete the one on the server. The Local Folders emails are kept in your Profile on your computer, these folders/emails are not on the server, unless you chose to keep a copy of them on the server. Pop mail accounts cannot see the folders on the server. They only access the server Inbox folder and download emails not previously downloaded to the mail account Inbox in Thunderbird. These emails are kept on your computer in your profile folder. You can select to keep a copy on the server or not. You can choose to delete emails off your computer and off the server or not. If the mail account is gmail , have you subscribed or even synchronized to see the 'All Mail' folder ? Gmail's all Mail folder is their Archive folder, it keeps a copy of all of your non-deleted emails. So, you do not need to subscribe to see this folder as it only shows you what you can already see in other folders. It doubles the disc space. Please read section on 'All Mail' at this link. * http://kb.mozillazine.org/Using_Gmail_with_Thunderbird_and_Mozilla_Suite You do not have to download/synchronize the entire folder. You could select to only synchronize the most recent xx days of emails. see info here: * https://support.mozilla.org/en-US/kb/imap-synchronization#w_configuring-synchronization-and-disk-space-usage