Making his first start since Jan. 23, Emery had a shutout going until Matt Stajan scored with 2:26 left.
The Flyers enter the Olympic break just one point behind the New York Rangers for fourth place in the Eastern Conference.
Despite winning six of their past eight games, the Flames are tied for the third-fewest points in the league.
The teams resume their regular-season schedule on Feb. 27.
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