They should complete their sentences for the crime of which they were convicted.
Suppose a person gets a traffic ticket for failing to stop at a stop sign. He is convicted and fined $50.00 and court costs. The city then decides to move the stop signs to the other intersecting street allowing traffic to flow where the person had blown through the stop sign. Should that person get his $50.00 and court costs refunded? Of course not. Changing the stop signs does not change the fact that the person broke the law.
If the Gubber-nor Moonbeam wants to pardon all those people, he can do so.
State governors can pardon federal felons? Cool!
that's a false equivalence. A more accurate analogy would be passing a proposition outlawing stop signs. Or perhaps the traffic control sign in question was removed because it didn't conform to standards (e.g. Speed limits in CA are required to conform to a documented engineering study). But it should be made obvious in the proposition to avoid embroiling the state in pointless legal action.