After upgrading to version 1.15.3.858 on Ubuntu 16 LTS, PMS seems unable to find the Application Support folder. Based on resources being used, it seems like it started using /var/lib/plexmediaserver/Library/Application Support.
Accessing the server through the web interface after the upgrade shows all of my libraries gone and the preferred server name defaulted back to the host name of the computer. It is as if I have lost all settings.
I tried changing the /etc/defaults/plexmediaserver file to indicate the value of PLEX_MEDIA_SERVER_APPLICATION_SUPPORT_DIR directly, but this did not change the behavior.
As of Ubuntu 16, /etc/defaults/plexmediaserver is obsolete due to systemd.
If you previously modified /lib/systemd/system/plexmediaserver.service, this was incorrect modification. The package manger overwrites it with each installation.
To make your changes persist across installations, please see the instructions here for systemd