Database and settings wipe on reboot

I have been running Sonarr on Raspbian for a while but have encountered a strange issue recently. Every time I reboot the server which is running Sonarr, the database and all application settings are wiped. I am currently using the init.d script provided here to start Sonarr. I initially used Upstart but I got tired of working around Raspbian trying to remove it during software updates.

In the init.d script, I used the below variables. Does anyone know why sonarr would wipe the database, settings and any backups at each reboot? Any help would be much appreciated, thanks!

    ############### EDIT ME ##################
# path to app
APP_PATH=/opt/NzbDrone

# user
RUN_AS=nzbdrone

# path to mono bin
DAEMON=/usr/bin/mono

# options for mono
DAEMON_OPTS=""

# Path to store PID file
PID_PATH=/home/nzbdrone/.config/NzbDrone/
############### END EDIT ME ##################

It definitely wouldn’t. Is /home/nzbdrone being cleared on each reboot? Disable the init.d script and reboot, if /home/nzbdrone/.config/NzbDrone/ isn’t still there that would be the issue.