I had the same effect today when upgrading from 4.2.4-42 to 4.2.6-7. For some reason my configuration was stored in "/home/tvheadend/config", but "/etc/sysconfig/tvheadend" has set the config folder to "/var/lib/tvheadend/config".
I have compared the content of both folders, and to me it seemed that the folder in the home directory stored the configuration that was used for 4.2.4 ( passwd, bouquet etc... ). For my setup I just needed to change 1 line in my home config and to copy the whole "/home/tvheadend/config" folder to "/var/lib/tvheadend/config"
The line that I have changed in my config file ( "/home/tvheadend/config/config" ) was the version string taken from the config file in "/var/lib/tvheadend" ( "full_version": "4.2.6-7~g5613551.el7.centos" ).
# stop tvheadend
systemctl stop tvheadend
# backup new config directory
cd /var/lib/tvheadend
mv config config.bak
# copy config directory from home/tvheadend ( moving would also be ok )
cp -r /home/tvheadend/config config/
# start tvheadend
systemctl start tvheadend