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If i understand your question properly, the answer is Yes.
The setup of incoming mail addresses tells you that it wants the mailbox to be empty, If you point an incoming mail setup in WHD to a mailbox that is not empty, it will make you click a button that tells it to go ahead anyway (it gives you a button for "Confirm Settings" that you must click). If you do that it will most likely process ALL tickets in that Inbox into tickets AND delete them from the mailbox.
Like kellytice said, it will attempt to make tickets out of all the email in the inbox based on your settings. It will either make a ticket or reject the email but either way afterwards, it will clear the inbox. Also just a note... The email inbox you use should be dedicated to email that is only intended for WHD to create tickets out of. Using the mail account for anything else in addition to WHD ticket support opens up a totally new can of worms. Doing so can risk possible infinite looping if people use the email address as a cc or in an email capable printer for example. Just a friendly word of caution.