But it appears that after a public outcry in Quebec over the switch, the plan to sell the valuable works was spiked.
Seven months after they were packaged up and sent to a storage facility, the paintings "Canada West Canada East" have still not been put back on public display.
The debate over what to do with the paintings, valued by the department at $90,000 each, is detailed in a package of documents obtained under Access to Information legislation.
With about ten days' notice last June, bureaucrats were instructed by Foreign Affairs Minister John Baird's office to put up a portrait of the Queen in the lobby of the Lester B. Pearson building in downtown Ottawa.
The large wall that all visitors see as they enter the area was redesignated as the "Sovereign's Wall" in time for a visit by the Duke and Duchess of Cambridge over the Canada Day weekend.
Bureaucrats initially suggested that the Queen and the Pellan paintings — which broadly depict western and eastern Canadian landscapes in vivid colours — could share the same space. Pellan painted the pieces during the Second World War for the new Canadian mission in Brazil, and they have hung in the Pearson building for nearly 30 years.
But the idea of Her Majesty going shoulder to shoulder with the Pellans was quickly quashed by the Conservatives.
"There was a lot of discussion between the Minister and Deputy Minister on Friday, and despite other recommendations, they want to go with the idea in their message at the very end of this," said one facilities manager, referring to an email by Baird's adviser to "take the red portraits down."
A month later, a media response prepared by the department — but never released — revealed plans to sell the paintings.
"As per the department's artwork policy, the paintings were appraised and deemed too valuable to be taken care of by the Department's Visual Arts Program," the document reads.
"They are currently in the Department's art storage facility, where they are being cared for until they can be offered to various Canadian museums or other government collecting agencies for purchase and display."
Internally, bureaucrats mused about the advisability of selling off the works.
"Should we reconsider if these two paintings should be taken off the list of art for sale/disposal?" wrote one civil servant in charge of the art collection.
Another wrote, "We should perhaps revisit the (communications) plan, and add some strategic considerations in regards to the paintings that are slated for sale .... there may be further media interest."
The decision to remove the Pellans in favour of the Queen's portrait was roundly criticized by Quebec pundits as insulting and quasi-colonialist. As recently as Christmas Eve, Le Devoir's editorial cartoonist featured Santa giving a joyful prime minister a portrait of the Queen.
Pellan is one of the best known painters in the province, with several public spaces and a federal riding named after him. He was a contemporary of Paul Borduas and Jean-Paul Riopelle, but parted ways with them on Quebec sovereignty.
By late August, plans began to circulate within the department to put the paintings up somewhere else — perhaps in another part of the building's lobby. Baird's office, however, has kept secret any details about the fate of the Pellans.
"The Government of Canada has no plans to sell these paintings," Baird spokesman Joseph Lavoie tersely responded last week.
The decision to remove the Pellans sparked a handful of critical emails to Baird from Quebecers.
One citizen wrote "...that this government acts like a servant of her Majesty, as if we were British subjects, is deeply insulting!" — then signed off his location as "Quebec, England."
Another wrote, "I'm a federalist who is beginning to think otherwise faced with an anti-Quebec anglophone such as yourself. It's decisions like the one you've just taken that allow the rise of separatism in Quebec."
"Now, you spit on our nation and confirm to the entire world the feeling of subjugation that has rankled us since the Conquest," wrote another. "Kate and William could have surely spent a few days on foreign soil without seeing a photo of 'Mommy Elizabeth.'"
Thomas Delworth, a retired Canadian diplomat who oversaw the hanging of the Pellans in the Pearson lobby, said the paintings should be displayed in a place where the public can enjoy them.
"I don't know of any pair of paintings anywhere in the National Gallery or anywhere else that in one fell swoop gives you a total image of this country from sea to sea," said Delworth, who retired in 1993.
"That's why they're important, and they belong to the Department of (Foreign) Affairs. They tell the story of Canada to all the hundreds and thousands of people who walk through the doors and see them on that wall."