I faced a similar situation where InnoDB got disabled after a mysql-server upgrade. The query “show engines” didn’t display Innodb. Following this link fixed the issue for me.
/etc/init.d/mysql stop
cd /var/lib/mysql/
ls ib_logfile*
mv ib_logfile0 ib_logfile0.bak
mv ib_logfile1 ib_logfile1.bak
/etc/init.d/mysql restart