When you say “I am importing from a POP3 account” did you import your messages and folders from an existing mail client’s message store (e.g. An Outlook pst file) or are you just syncing to your email account on your ISP’s mail server? If it’s the latter, you need to be aware that the POP protocol can only retain copies of your Inbox mail on the server, so there will not be any copies of sent items etc. on their server. In order to maintain and sync all folders you need to be using the IMAP protocol.