Okay, I reverted the PBX to the snapshot I had prior to the update last night.
I rebooted cleanly, and made sure everything was working normal, and then I made a new snapshot.
After the snapshot I rebooted again just because I want to make sure everything is as normal as possible. Everything was working fine.
I then ran yum update
from a SSH session. It took almost an hour. I have never seen this happen before. The system was last updated sometime in April or early May.
When the update was done I issued the reboot command from the SSH session.
That gave me a weird error message that seems like some script was still running. So I exited that session.
I still had a separate SSH session running to see if I got the above MySQL errors this time. Yup, I did.
Here is everything from the yum update session it is quite long: hastebin
Eventually, it did reboot after about 5 minutes of those errors.
Everything came up normal and was working. I waited about 30 minutes and then issued a reboot from SysAdmin within the web GUI.
I did not get MySQL errors, but I did get this. Again like 5 minutes to actually reboot.
I had a separate window up and it showed /sbin/reboot executing the entire time.
I waited 20 minutes and issued another reboot from the web GUI, and look what happened.
At this point I assume it will fully reboot in 5 minutes as it has been.
edit: yup.
Edit 2:
For reference this was FreePBX 13 installed back in 2016. It was upgraded to FreePBX 14 via the upgrade script in 2017 (October I think).
The system has 6 users and a few test extensions.
The system is running on a $5 Vultr instance.