Also not to keep beating a dead horse here but there is another system that had a similar symptom that I’ve noticed for a very long while that has something in common with this problem, a cron line missing in that exact same cron file. It’s the scheduled backups.
They would randomly stop working I’d say at the same rate that the certificate renewals would stop working. When we would check the backup line would be missing from that cron file. Saving the same backup job would add the line back in but then after a while it would disappear again and backups would stop.
Somebody recently mentioned that same symptom here: Scheduled Backup not working
It’s been working a lot better for us on newer versions of FreePBX (so 16 and up) but for sure it was a pain for a very long time for us on older FreePBX systems as well.
This is all to say, there is something for sure removing these cron jobs from the cron file seemingly randomly, I was just never able to determine what.