This is what I ended up doing:
- Shut down the MySQL server.
- Made a copy of /var/lib/mysql (tar -cpvzf mysql.tgz /var/lib/mysql)
- Copied /var/lib/mysql from the backup to replace the current /var/lib/mysql
- Turned on MySQL server.
- Mysqldump of needed database.
- Shut down MySQL server.
- Restored /var/lib/mysql from the tgz file I made in step 2
- Turned on MySQL server.
- Inserted data of needed database from mysqldump file created in step 5.
Hope this helps anyone faced with the same dilemma!
More Thoughts I highly recommend turning on innodb_file_per_table=1 in my.cnf. This should be done between steps 8 and 9 in the list above.