Hmm, look at your chrony.conf file. See if there is a definition for the location of the pidfile.
Mine shows:
# chronyd writes its process ID to a file. If you try to start a second
# copy of chronyd, it will detect that the process named in the file is
# still running and bail out. If you want to change the path to the PID
# file, uncomment this line and edit it. The default path is shown.
pidfile /opt/var/run/chrony/chronyd.pid
Your might be different. If you do see this, try to remove the chrony.pid file.
If there is no pidfile, double check chrony is not running.
$ ps | grep chronyd
If not chronyd and no pidfile - try the restart one more time using the CLI. It might complain as to why it won't start. Make sure you have chrony.conf setup in /jffs/addons/ntpmerlin.d (Jacks default is fine)
$ chronyd -r -u nobody -f /jffs/addons/ntpmerlin.d/chrony.conf