Thanks for your fast and sorry for my late response (too much to do and too little time).
Your sugestion and this one https://moodle.org/mod/forum/discuss.php?d=273400 helped us to find a solution.
Odg: Re: "MySQL server has gone away" error when making backup
by Miha Osojnik -
Number of replies: 2
In reply to Miha Osojnik
Re: Odg: Re: "MySQL server has gone away" error when making backup
by Ben Laor -
Can you share the specific solution you used? i'm having the same problem and can't seem to fix it
In reply to Ben Laor
Re: Odg: Re: "MySQL server has gone away" error when making backup
by Ben Laor -
After trying all the offered solutions (increasing max_allowed_packet, adding $CFG->dbsessions='false', and updating all tables to Barracuda) The solution was found by going through the course's units and deleting them one by one until we could perform a backup, and we found the problematic content (probably was corrupted).
Not the fastest solution but the best in lack of a better one.