Simply download the latest version of PMS and dpkg will take care of the rest:

Download PMS in a temp folder:

http://plex.tv/downloads

wget http://downloads.plex.tv/plex-media-server/0.9.11.16.958-80f1748/plexmediaserver_0.9.11.16.958-80f1748_i386.deb

Run dpkg which will take care of overwriting your current version of plex retaining all settings:

dpkg -i plexmediaserver_0.9.11.16.958-80f1748_i386.deb

Done!