It's mission impossible, well, close to impossible. The scooping activities will introduce O2 into the anaerobic layer, if not mixing each lkayers already. If the transport duration is rather short, the sand bed nitrifying bacteria will be preserved. The nitrogen fix fuction will still continue into the new tank, but the anaerobic layer will have to be re-developed.
Since you will be losing the anaerobic zone, you might as well do a light rinse of the sand before you put them into the new tank. You will be amazed with how much junk is trapped within.