Perhaps the OP could tell us which airline his reservation is on for each segment and his ticket type.

From Vancouver, BC (YVR) to Japan the only airlines I know to service the direct route are Air Canada and it's Japanese Star Alliance partner, ANA; and One World's Japan Air Lines.

If it's either of the Japanese airlines then there might be an option to reroute direct to Japan from a U.S. gateway.

If he's on Air Canada then his ticket exchangeability/refundability depends upon the fare class paid.

However, OP must also ensure that he meets Japanese entry requirements regarding any legal problems he may have had.

Although the OP may have "got away" with entering Canada by car in the past while banned, this is extremely unlikely at airports, YVR being quite stringent.