Hi,
Use and change:
sh /script/mysql-convert --engine=MyISAM
sh /script/mysql-convert --engine=InnoDB
to have both, the old and new, database engines the same. Better convert to InnoDB--->MyISAM before.
Before doing anything anywhere, make a copy of /var/lib/mysql/* - for an extra copy of all directories - of databases under it in case anything goes wrong. then you can play with such conversions.