Not sure I followed completely the description of your layout before and after the helix. However, conceptually it seems to me that all you need is an AR circuit wired into the helix, with the helix isolated from the approaching (entering/exiting) segments. Be sure your feeders to the helix are all wired from the power bus through the AR, and include feeders near the ends of the helix (where the short circuits that the AR will correct will be sensed).
Unlike DC, the DCC system is not as "polarity" sensitive as your description suggests. An AR circuit will automatically adjust the phase cycle of DCC to avoid the short that would otherwise occur. Your trains should cross the gap into/from the helix indifferent to the change in phase cycle.