I would use nano to edit your my.cnf and make sure you save. Perhaps if you stop MySQL first and then edit it, save it and restart MySQL. So something like this:
service mysql stop
nano /etc/mysql/my.cnf
<edit the max_allowed_packet><Ctrl><X>
service mysql start
You can also exclude the MySQL DB (check the TKLBAM docs for details) if you wish which will at least allow you to get your other data back, but obviously won't solve your issue.
Have you edited it from the commandline
I would use nano to edit your my.cnf and make sure you save. Perhaps if you stop MySQL first and then edit it, save it and restart MySQL. So something like this:
You can also exclude the MySQL DB (check the TKLBAM docs for details) if you wish which will at least allow you to get your other data back, but obviously won't solve your issue.