British Airways has experienced similar twice this month! The crews from the scheduled BA31 flights, arriving in Hong Kong on the 1st and 5th September respectively, were all placed in long-term quarantine, apparently due to one passenger on each flight testing positive for Covid on arrival.
BA have long told their crews, and crews have been seeking assurances for some time, that they had agreed procedures with the Hong Kong authorities to avoid long-term quarantine issues for crew. However, precisely what those procedures are has not been told to BA crews.
The quarantining of these two BA crews this month, inclusive of pilots and cabin crew, seemed to set the cat amongst the pigeons at BA. When the incidents were queried on the company-specific forum of the British Airline Pilots' Association (BALPA) website, a moderator responded that both BA and the UK government were in contact with the Hong Kong authorities, and BALPA forum users should not write anything that might undermine those talks. If BA was so sure of it's apparently in-place procedures, it seems odd that it would need further negotiation with Hong Kong, and have to include UK government involvement.
An agreement of sorts must have been made, as BA then flew a freighter aircraft out to Hong Kong, with the intention of collecting both crews. That aircraft returned to London on 9th September.
Interestingly, the Hong Kong Centre for Health Protection publishes a continuously updated document which lists the arriving vessels involved in cases having Covid detected on arrival. The document has the long-winded title of "
List of Flights/Trains/Ships/Vehicles Taken by Confirmed or Probable Cases of COVID-19 From 2 Days Before Onset of Symptoms, Or Taken by 2 or More Confirmed or Probable Cases During Incubation Period"
It can be found here:
https://www.chp.gov.hk/files/pdf/flights_trains_en.pdf
As of the time of writing, the published data runs to 11th September, and includes the two BA flights. The link in the opening post, to a Toronto Sun article states that "The four-person cargo plane crew were detained Sept. 9 after a pilot allegedly tested positive for COVID-19". However, the Air Canada flight is not (yet) listed.