Backing up and restore tokudb files on a new mysql installation

Hi,
In reference to my this post https://www.percona.com/forums/questions-discussions/mysql-and-percona-server/48401-upgrade-bug-tokudb-gone-missing-or-tokudb-is-buggy. Is looks like I have to restore the whole tokudb. Is there any way I can disabled innodb? So I am going to yum remove the current mysql and reinstall again. In the meantime I still have my current db directory with all the tokudb data files. So once I create the refresh installation I just create a new database and can I replace in those files and restore my db via this method?