Sure, it may sit in the depths of HR until the end of time, but you can be sure of two things: One, your former boss (and future reference) will read it and be impressed. And two, if you ever decide to come back to your company (hey, it happens), it's a very good thing that last thing on file is a great, professionally written resignation letter.
Prepare for It. Like the situation above, you should go into the conversation knowing how you'll respond if your boss asks you to extend your notice. If you've landed another job offer and have already set a start date, this may not be possible__so practice sticking to your guns: "Because I have a new opportunity lined up, my last day here is firm.