Yes, you could potentially create a full fledged cycle. All the crap trapped in it could be released into the tank. Even if you try to siphon it all out, you will inevitably miss a bunch.
A ton of good bacteria and critters live in the substrate. Taking it all out at once would totally upset the entire balance of the tank. Pottentially not allowing the proper breakdown of the :pooh: released.
IMO, I would change out a section at a time. This allows the new section to become live and compensate for the amount that you take out next time.