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.
Per the Hinterland Rules, Chancellor does not trigger Tunnel
This ability does not function if cards are put into your discard pile without being discarded, .... when your deck is put into your discard pile, such as with Chancellor
Per Dominion base Rules:
"Discard" – unless otherwise specified, discarded cards are from the player’s hand. When a player discards a card, he places the discarded card face-up onto his Discard pile. When discarding several cards at once, the player need not show all cards he is discarding to his opponents, but player may need to show how many cards he is discarding (for example, when playing the Cellar). The top card of a player’s Discard pile is always visible
So, you are not discarding the Tunnels in your deck when you activate the Chancellor: you are simply moving them in the Discard pile.