at the bottom of your sand bed you may have pockets of anaerobic bacteria. This is the bacteria that changes your nitrates to harmless nitrogen gas. If you disturb that, it can cause very nasty parameters swings as Oxygen is introduced. There is also the material that is trapped and being slowly taken care of by bacteria, bristleworms, etc. By stirring up the sand, you reintroduce this into your water column. Now, if you stir your sand regularly this isn't so likely. But if you don't, then the odds increase. That's why I never stir mine up.