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by lunarg on October 17th 2012, at 09:21

Be careful when deleting a POP3-account in Apple Mail. Doing so will also remove all messages from the folders Inbox, Sent items and Trash, even if they are no longer on the server and only available offline.

To prevent this from happening, move/copy all messages to folders created inside the On My Mac section. These are folders that are kept locally and will not be affected when removing accounts. After which, you can safely remove the account.