If the police checks aren't being included with the application, be sure to send a letter explaining why. If processing through an overseas embassy, they will always ask for them again before they do the assessment. It delays processing, but if you can't provide them and want to get things rolling, then just wait to send it (because you have to send the original) until after you receive the letter from the embassy requesting it. You'll need your file number, etc., to make sure it's not lost.
If you're applying inland, they're not going to look at the ap for 11 months, so chances are you'll have to do another anyway. Again, include a letter explaining why it's not there, and be ready to submit when they ask for it. In both cases, remember, the clearances can't be more than 3 months old when they are submitted, so timing is important.