I believe the intent of the discount program is for Helix Native and a Helix device to be used in tandem. Understandably, Line 6 wants to discourage the practice of anyone buying a Helix device, claiming the Helix Native discount, and then immediately returning their device to the retailer for full refund.
So the status of the Helix Native license depends on the timing of its purchase and the subsequent sale of the associated device. I think you need to retain ownership of your Helix device for some time (180 days I believe) after purchasing Helix Native at the discounted price before your Helix Native license becomes permanently vested with your Line 6 account. Meanwhile the Helix Native license remains associated with the device.
After that period you can sell your Helix device and you have the option to transfer your Helix Native license to the new owner, which of course means you can command a higher selling price. Or you can keep your Helix Native license and the new owner of the Helix device is unable to claim the discount. If you return or sell your Helix device during that period your Helix Native license is revoked (I.e. removed from your Line 6 account and ‘given away’ in the language of Line 6 Support since the license remains with the device) and the new owner may claim the discount. Of course in practical terms Line 6 doesn’t know that you returned or sold your device; they will only revoke your license when the new owner registers the device with what used to be your serial number.
It sounds like you may be wanting to sell your Helix device within the specified time period. Is that the case? If so your Helix Native license is not yet permanently vested with you; it remains associated with your Helix device. Accordingly you can sell your device at a higher price and use that to purchase a new discounted Helix Native license associated with your new HX Stomp.
Alternatively you could keep your current Helix device until your Helix Native license is permanently vested with you, sell it later at a lower price, and not have to purchase a new Helix Native license when you get your HX Stomp. In that scenario a discounted and unused Helix Native license remains associated with your HX Stomp which increases its resale value.
At least, that’s the way I understand it. Could be wrong.