that's a bit worrying...

The trip is in December, and there is only a 1-hour connection time between the flights in NRT. Initially I tried to book the ticket from Air Canada and they quoted me the same itinerary and considered the connection time legal.

However, for some complicated reason I only purchased the YVR-NRT segment on AC and redeemed my Aeroplan points for NRT-TPE on NH.

If I link the two itineraries and the YVR-NRT flight does arrive late, will NH know that I am on a late-coming AC flight? Or will they consider me as no-show and I lose my ticket entirely?

It's less of a problem if they don't provide me with accomodation for the night, but it will be disastrous if my ticket gets invalidated.

I was actually on a similar itinerary(YVR-NRT on AC, NRT-TPE on JL) last December, but both segments were on 1 ticket. The AC flight came in 6 hours late(the day that YVR got paralyzed with the snowfall..) into NRT. As we got off the plane, there was a welcome booth set up by ANA ground staffs at the gate, with free hotel and flights rebooked for next morning for everyone who missed their connection. However, since this time I am on two separate tickets so I don't know if ANA will still be this nice. Would travelling in J and being an SE help?