I would say we have no idea. Sure, he was acting Knight Commander for the span of at least, what, 10 minutes while you killed Meredith (prob longer on Nightmare
). After Hawke split Kirkwall/became Viscount/ess...? Who knows how long that lasted.
Going by the math of DA2 (and that makes my head spin almost as much as how Anders can be in 2 places at the same time), it was 3 years between the events of the Act 3 finale and Cassandra's interrogation of Varric. Somewhere in that space of time, Hawke disappeared. After the battle with Meredith, if Hawke becomes the Viscount, we see Cullen kneeling. If, however, Hawke sided with the mages, Cullen looks at Hawke with trepidation and allows the party to leave. In this last scenario, it seems as though Hawke and company leave post haste, which would leave Cullen with quite the mess on his hands. And Cullen does relieve Meredith of command, which would make him Knight Commander pro-tem and he would remain so until some sort of word arrives from the Divine. Since we won't be travelling to the Free Marches (which blow my theory on how we meet Cullen all to hell), something after Cassandra's interrogation must have happened and Cullen left Kirkwall.
OK, that all made sense in my head. 