If you mean, can you use the isolated spa piping to clean out the water mold in the filter and spa piping, prior to draining your main pool, then the answer is maybe. It depends on your piping and valves. If you want to try that, I'd

1. Drain the pool & spa.
2. Replace the sand.
3. Refill the spa, and superchlorinate.
4. Drain the spa, refill pool and spa and start the Baquacil based cleanup.