While continuing his career in fiction filmmaking, Flender never lost interest in documentary. In 1998 he began filming a musical portrait of the Boston-based rock band The Upper Crust. Unforeseen dramatic developments within the band led Flender to continue shooting on and off for the next five years. The resulting documentary, Let Them Eat Rock, played film festivals in 2005 and 2006 to mostly positive notices. Following the 2010 Tonight Show conflict, Flender joined Conan O'Brien (whom he knew since their days at Harvard) on the road, as part of the Legally Prohibited from Being Funny on Television Tour, and filmed the ongoings behind-the-scenes, onstage and between shows. The documentary, titled Conan O'Brien Can't Stop, was released in select theatres on June 24, 2011, which Roger Ebert featured on his list of best documentaries of 2011.

Flender continues to direct in multiple genres, having directed episodes of the comedies Suburgatory and Super Fun Night in 2014, the drama Finding Carter and multiple episodes of the thriller Scream in 2015 and 2016.

Over the next decade, Flender’s feature directing credits included Leprechaun 2 for Trimark, which currently holds a 0% approval rating on movie review aggregator website Rotten Tomatoes; and the Columbia Pictures release Idle Hands. Flender also became a busy Director of television episodes and pilots. TV credits include multiple episodes of the comedies The Office and Ugly Betty; dramas that include Chicago Hope, Gilmore Girls and The O.C.; and horror with HBO’s Tales From The Crypt. As a Writer, Flender’s credits include Tales From The Crypt and the feature film Roger Corman’s Dracula Rising.