How should I connect a Wink relay when two circuits are involved?
It is always safe to leave a hot wire capped off with a wire nut. However (as Harper says), you must also disconnect and cap off the corresponding neutral wire. 

Find and remove the wire nut connecting the neutral that you want to discontinue. Having separated the wires, cap off the one leading to the circuit breaker. Connect the one from the light to the neutral wire nut that will remain in use. 


fig.1a, left: Existing circuits; fig.1b, right: Modification for Wink 2-load control. 

You should add up the total loads on each of the two circuit breakers, and power the switch from the one with the lighter load. The illustration assumes that the power feed on the right was from the more heavily loaded breaker. 

You might consider leaving a label "no longer needed" taped to the wires, but that is not required, and any future maintainer who sees the two loads and the double gang box will not be horribly confused by what you did.