This may be getting at the problem. I know some on here advise changing substrate with fish in the tank, but that should never be done when it involves the entire substrate.
The substrate (whatever material, gravel or sand) is home to a thriving host of various bacteria species. There are aerobic and anaerobic. Both are needed. Disturbing the aerobic areas, like you would with regular siphon cleaning, is not going to cause issues. Disturbing the anaerobic zones can be deadly. I know, I have done it (not with fish in the tank). The black gunk is smelly to say the least. I would never do this with fish in the tank. All areas under rock, wood, other decor tend to be anaerobic. Any areas you never get to will also likely be anaerobic.