You can clean the sand bed, but you should never do the whole thing at once. At best it will send your nitrates soaring, more likely you will cause your tank to recycle. People who do like to clean their sand beds will clean a small patch with every water change, and over the course of a couple months every section will be cleaned.
Its best, like SeaBee said, to get critters to stir the sand bed for you. The best are nass snails. Your lfs might try and sell you a sand shifting star fish, but with your nitrates as high as they are, it will most likely die. Starfish are extremely sensitive to nitrates. You could also look into getting a sand shifting goby to help keep the sand bed in check.
Also, when you do get the snails, i would take an extra long time to acclimate them because of the high nitrates. All invertebrates are extremely sensitive to nitrates, which are toxic to them. With the snails you might be able to acclimate a few to your levels enough to survive and start cleaning the sand bed.