Air Canada extended a travel alert affecting airports in Central and Atlantic Canada Thursday, warning passengers to expect more flight cancellations and delays as it and other airlines worked to clear the backlog in baggage and passengers caused by severe cold weather and winter storms earlier this week.

The travel alert affects Toronto, Ottawa, Montreal, Halifax, St. John's and several U.S. northeast airports, including Boston and New York.

Air Canada said it was still in the process of clearing the backlog created when a sudden and atypical freeze crippled Toronto's Pearson International Airport overnight from Monday to Tuesday and similarly severe winter weather wreaked havoc on travel throughout parts of Eastern Canada and the U.S. 

The weather-related disruptions left thousands of passengers stranded and sleeping at various airports for days. More than 600 flights were cancelled at Pearson, a major flight hub for Canada and the U.S., on Tuesday, creating a domino effect at airports across Canada.

Air Canada said it extended the weather alert because "winter operational conditions" were still affecting some Air Canada flights and Air Canada Express flights operated by Jazz.

It did say, however, that it increased capacity on a handful of domestic flights scheduled to fly in and out of Pearson on Thursday and Friday.

"For example, today (Thursday), we put a 200-plus seat 767 on a flight between Toronto and Ottawa and back that before was a 97-seat Embraer aircraft," spokesperson Peter Fitzpatrick said in an email to CBCNews.ca. "For tomorrow, we have put on some large Boeing 777s for flights to Halifax, Edmonton, Calgary and Vancouver to replace smaller aircraft.

"As well, with the flexible re-booking policy, some people are deferring discretionary travel, and this frees seats for people who wish to still travel."

Travel backlog in Toronto clearing

WestJet added 14 additional flights on Thursday to help clear its own passenger and baggage backlog and chartered two planes, including a 470-seat Boeing 747 that will fly people and 1,100 pieces of luggage from Toronto to Calgary Thursday afternoon. WestJet spokesperson Robert Palmer also said that by Thursday afternoon, the airline had rebooked all of the customers who had been unable to travel because of the disruption earlier this week.

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Canadian Coast Guard icebreaker Pierre-Radisson clears the ice flow on the St-Lawrence River in Quebec City Wednesday. Extreme cold and strong winds crippled many parts of Canada and the U.S. this week and made travel of any kind difficult. (Jacques Boissinot/Canadian Press)

"So, we’re not out of the woods yet, but we’re certainly pleased to be able to say that we don't have anyone who does not have a flight — although they may not have flown yet," he said.

Porter Airlines issued a weather advisory for St. John's on Thursday morning, saying passengers may face delays and cancellations.

Pearson spokeswoman Trish Krale said flight schedules were mostly back to normal Thursday, with roughly 40 scheduled flights cancelled — down from about 400 on Wednesday. Passengers are still being advised to check their flight status before heading to the airport.

Krale said the airport continues to recover from the disruptive weather.

"There are still some things in the terminal that are having to be dealt with in terms of bags and re-booking people."

Baggage still piling up

Some frustrated travellers at Pearson who were still trying to trace their luggage expressed concern that there was not adequate security and airline staff to watch over the large number of unclaimed bags that were piling up in the airport's baggage areas, leaving them vulnerable to potential thieves.

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Frigid temperatures and icy conditions on the tarmac at Pearson slowed offloading operations and caused a baggage backlog. (Eric Foss/CBC)

But Palmer said WestJet has had no reports of stolen baggage and has assigned staff to watch over the bags and to escort people searching for their luggage into its baggage area in Terminal 3.

"Obviously, we’ve been watching over them as closely as possibly given there's hundreds and hundreds of them," he said.

Fitzpatrick said Air Canada, which operates out of Terminal 1, was "marshalling bags and moving them to a secure area" and that there were cameras and police throughout the airport to help maintain security.

The bags left in the domestic baggage area of Terminal 1 can potentially be accessed by people who have not cleared security, but GTAA spokesperson Corrinne Madden said airport security personnel are supposed to be monitoring the area along with airline staff.

The international baggage carousels are in a customs-controlled area, she said, and people who want to search for their baggage there have to be escorted into that part of the airport.

Bags arriving at destinations without passengers

The baggage disruptions have also meant that some baggage was sent on to destinations even though the bag's owner did not make it on the flight, a practice that under normal conditions would be considered a security risk.

The backlog in baggage was caused by the fact that icy conditions on the tarmac and temperatures of -40 C with wind chill Monday night and Tuesday morning slowed down the process of bringing planes up to the gates and offloading passengers and baggage. When gates got backed up, airlines decided to offload passengers but keep the luggage on the planes until the ground crews were able to catch up and unload them.

"When a gate became available, we would push a plane up to the gate and people would walk off the plane, but we had to leave their bags on the plane, because it would have taken hours to get bags off, and, meanwhile, there were other planes behind them with more people on those planes for hours and hours," WestJet's Parker said.

Eventually, the backlog got so bad that the airlines, together with the airport authority and Nav Canada, decided to halt scheduled flights from North American airports at their points of departure for two hours.

With files from The Canadian Press