POP works very differently from IMAP. POP mail accounts can only download from server Inbox. They do not see anything that resides in any other server folders. Pop folders do not synchronise with server folders. If the POP mail account had settings to 'Leave copy of message on server' then the server will still have a copy. When you delete anything from a POP mail account, it does not necessarilly mean it has been deleted off the server. If this is a gmail account or one that uses a similar gmail format then, it may have deleted a label but not the email, so emails will still be in the original folder called 'All Mail'. IMAP means you can subscribe to remotely access any of the server folders and see emails. All folders synchonise with server to show you what is on the server. This means any emails filtered into server 'Spam' folder will now be visible. When you delete in Imap, emails should be put into the server 'Trash' (or whatever the server calls that folder). Emails you delete in Thunderbird will be deleted off server as server folders are one and the same as those in imap mail account. https://support.mozilla.org/en-US/kb/imap-synchronization Only you will know what emails are relevant or not.