From the wording of Chancellor, I would assume no because it doesn't mention that you're discarding those cards, but I don't have access to the rules at the moment to see if either base or Hinterlands rules cover this.
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Per the Hinterland Rules, Chancellor does not trigger Tunnel
Per Dominion base Rules:
So, you are not discarding the Tunnels in your deck when you activate the Chancellor: you are simply moving them in the Discard pile.