Just done.
It gives:
Fetching FreePBX settings with gen_amp_conf.php…
SETTING FILE PERMISSIONS
Permissions OK
Removing any dangling symlinks
Dangling symlinks removed
Still System Status → System Overview shows the informative notice (I can ignore it) as nothing happened.
Should I restart the system? I did an amportal a r just to be sure.
Rebooted but still the informative notice about those 3 unsigned modules (Security Issue) is there.