Board Thread:Questions and Answers/@comment-26999015-20160302045654/@comment-1894786-20180425005035

Some people think the one-shot takes place before season 1, and that Agent Flynn was replaced with Chief Dooley in the fallout from his treatment of Peggy. Others think you can retcon the year it takes place (1946) to after Season 2, and that Flynn's presence is due to Chief Thompson's convalescence in Los Angeles after his gunshot wound (or alternatively, his death resulting from the same).

I'm of the mind set that it takes place post-Season 2, since Agents of SHIELD Season 4 implies that SHIELD was founded in 1949.