By default POPFile stores only the last two days of messages. Versions of POPFile prior to 0.18.1 run slower as your history grows, so it may be wise to clear the history occasionally to keep POPFile running efficiently or upgrade to 0.18.1 or newer.
It is entirely up to you how often to delete the history. A few words on this that you should be aware of though: If you delete your history often and then decide to reclassify a message that is no longer in your history, POPFile has no way of looking up that message.
Note: Deleting the history does neither modify your corpus data, nor does it affect any messages stored in your email client.