I have my aquarite plumbed right after the heater, so when in spa mode it still generates chlorine. I ran the system for four hours in spa mode, and then took a chlorine reading, which read only slightly darker than before(if my memory is and goodd)Unless you run your spa for many hours everyday, I dont think it would be a problem. If you are worried, you could just turn off the unit until your back in pool mode.

Of course your milage will vary depending on your spa size.