There was a smal discussion over on warshipsailors where a Russian freighter named Pechora is mentioned. Maybe same one you are looking for?
http://warsailors.com/forum/read.php?1,62255,62255#msg-62255
No definitive idea on Russian Commercial ship flag in 1940. There was no private ownership and if Pechora was a Soviet Navy Aux then maybe a Russian Naval Flag was used. Wikipedia has many references for Soviet Naval Flags.
Note: One source stated the ship spelled Pechora was actually the Patschura which became the German Raider "Pinguin".
(Statement: "Patschura... misspelling of the Name Petschora (German spelling) or Pechora (English)".
Good luck with your search. Sorry I could not help more.
Nino