or maybe you received a hacked one through trade?
If you're that worried, create a new profile, link a different Nintendo account to it. Let's call this profile B.
Now, restore your save into B. Use B's HOME (free) and deposit the Zekrom into B's HOME. It should get a tracker this way.
HOME let's you gain access to saves of other profiles. Let's call your main profile A.
Using B's HOME, access A's save, the now shift Zekrom into A's PC.
I didn't pay for Nintendo Online for my other profiles, but they all can use the free HOME just fine..