Critical Film Studies - S2-E19
Trivia: Abed mentions being an extra on the show "Cougar Town," and inadvertently soiling his pants out of nervousness. Abed actor Danny Pudi actually did appear in a cameo in the season two finale of "Cougar Town", which aired two months later. Although his cameo isn't quite as described in "Community", Pudi is visible in the background of one scene in-character as "Abed", and attention is drawn to him when he dramatically runs away at the end of the scene. (Likely because he soiled himself as described in "Community.").
Answer: The implication is that Jeff will still be teaching at Greendale after Annie and Abed leave. As for who became vice dean? It's never shown, since it's not really important to the series.
TedStixon