I actually got my passport back in time to travel. I sent a separate recorded letter requesting it along with a couple faxes. Followed those up with several phone calls and got it back fairly quickly. I understand that other people haven't been so lucky. It is really important that, if you are going to travel, if your permit is already expired, you carry the Certificate of Application with you. This doesn't guarantee that you won't have problems when you return to the UK, but besides being grilled heavily a couple times, I always got back in.
If you are traveling for work or important family business you shouldn't have a problem, especially if you can prove that. If you are going away for a weekend in Paris, they aren't going to like that.
Also, expect it to take at least 6 months. Even if they only have, by EU regulations, 6 months to process it, mine took closer to 9 and it was only after a series of complaints, to various bodies, that I got it back.